diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b85af3d --- /dev/null +++ b/.gitignore @@ -0,0 +1,40 @@ +*.pyc +__pycache__/ + +instance/ + +.pytest_cache/ +.coverage +.coverage.* +htmlcov/ +.vim/ + +dist/ +*.egg-info/ + +.DS_Store + +.mypy_cache/ + +.python-version + +# Jupyter Notebook +.ipynb_checkpoints/ + +# Logs +*.log + +# Zip +*.zip + +build/ +dynamodb_local_latest/ + +# Env files +.env + +# pickle files +*.pkl + +# venv +.venv \ No newline at end of file diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..ae3e1f7 --- /dev/null +++ b/Makefile @@ -0,0 +1,11 @@ +.PHONY: venv requirements test code-quality autochangelog + +venv: + rm -rf .venv + python3.11 -m venv .venv + +devready: venv + .venv/bin/pip install -r requirements.txt + @echo '###############################################################################' + @echo '### Do not forget to `source .venv/bin/activate` to use this environment ###' + @echo '###############################################################################' diff --git a/README.md b/README.md index e69de29..25c4473 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,10 @@ +# Variation Normalizer Manuscript + +## Set Up + +To create the venv: + +```shell +make devready +source .venv/bin/activate +``` diff --git a/analysis/civic/able_to_normalize_queries.csv b/analysis/civic/able_to_normalize_queries.csv new file mode 100644 index 0000000..3c33b6b --- /dev/null +++ b/analysis/civic/able_to_normalize_queries.csv @@ -0,0 +1,1870 @@ +variant_id query query_type variant_accepted vrs_id +2489 NC_000003.11:g.10191648_10191649insC genomic True ga4gh:VA.A34ZoIhq4xBuQbcE3bkj29n6diS6RzLB +1988 NC_000003.11:g.10191649A>T genomic True ga4gh:VA.JcEpDvhUtgDWU4A-bxqLUuczBNb8QqRf +2488 3-10191647-T-G genomic True ga4gh:VA.7nGd8dgHbqtxMHk_rLxrB6_IMAzJ8XnH +1986 NC_000003.11:g.10191648G>T genomic True ga4gh:VA.AmLtooLEvgdnEHD5YVWk6u1e2XBe7FiP +1987 NC_000003.11:g.10191649A>G genomic True ga4gh:VA.KIz00usFWEmJHNyqmVL61obfgfRPgOIa +2152 NC_000003.11:g.10191719C>A genomic True ga4gh:VA.LhSu37F8f7qk0QLH27y1HdrMjDbBWUV5 +2024 3-10191656-C-G genomic True ga4gh:VA.mMgxF5ZBI_mKkQlGzsngtBjfRendQJGb +467 KDR A1065T protein True ga4gh:VA.0t16H6jwVSU0sD45K7pp07qmX4301P56 +807 RUNX1 A107P protein True ga4gh:VA.zi8wZQKyKuBRMdo_L3S13xswDznXoAOH +3683 JAK1 A1086S protein False ga4gh:VA.zWoYigi80ulUVPy8jlfcKOYAIuz3gU_W +3030 BCL2 A113G protein False ga4gh:VA.D_DoojBG2xQC1JRVg9iFrYa8DpGtQQys +3342 KRAS A11_G12insGA protein True ga4gh:VA.nxQsSbH-LHRGyR_9D2ibbCv5tx_QbY4r +3544 PTEN A121E protein False ga4gh:VA.mm9qLtyAQuI3oTVe2VoNeAfKACEQaOCn +2028 NC_000003.11:g.10188221_10188222delinsAT genomic True ga4gh:VA.b9b0l6OTcy_-kiSBIuIfiEX-eZrNaLVV +3194 3-10188222-C-T genomic False ga4gh:VA.ANH--Chffdic6YowPig-3EU11iaICMQR +3528 PTEN A126D protein False ga4gh:VA.fLeUQzkuVFrmjHghLT0EtOK-YD46PGSp +3565 PTEN A126S protein False ga4gh:VA.cGcl1uKVuU0rjHPj9mahc4Xp2FQeNVZZ +4131 TP53 A138K protein False ga4gh:VA.0iRAeNi5T4I8dZuFDikJe7IYtDtWjue1 +3416 TP53 A138V protein False ga4gh:VA.Olf_c5TtZ_kMIsFzmfxPoZF8ygby0KoN +905 KRAS A146P protein True ga4gh:VA.hjl_YGBHQxFxm0BQJLJTCA1spswBcwC7 +906 KRAS A146T protein True ga4gh:VA.hVPeVv62KcteO9l7DAwwkfGX-lbaqJmR +322 KRAS A146V protein True ga4gh:VA.guI_A-mrvbeXAXruTGlmEYXdgHf1s8yn +820 NC_000003.11:g.10188302G>T genomic True ga4gh:VA.jOwuD9BZClYBYiRYaUlJKnenqhjzyuji +1744 NC_000003.11:g.10188302G>A genomic True ga4gh:VA.gY-P-24V_E0UKTtKB_iUNS3De-vKHaUr +2042 NC_000003.11:g.10188302delG genomic True ga4gh:VA.4gSd2WdkhaUVTjjUu5xizlRZ5Pm05BRk +4134 TP53 A161D protein False ga4gh:VA.XVbX35zXDxo7eI6Yg3zqzFOTbYWkwjDO +4116 TP53 A161G protein False ga4gh:VA.3ioUkqmo2Qb3b2iXhJjtb2hxosOV4DGy +1114 TP53 A161T protein True ga4gh:VA.TkDwOVc5QzkNG5ukbBY6WaX-ACaILav5 +4136 TP53 A161V protein False ga4gh:VA.hBMuLPtB_pWBKc0vM4jLQa0yumSiyHqK +3976 BRCA1 A1708E protein False ga4gh:VA.DsEPE4GdlgNHvLNjpbEuKGMjpfpYJMh0 +3994 BRCA1 A1789T protein False ga4gh:VA.v7DBjc8H2uetPf92FdbDUoAZSJQyRbqm +2929 PRPS1 A190T protein True ga4gh:VA.yHSoAvoa5NvBGH5MbWdWBCqm1OdeiP83 +2928 PRPS1 A190V protein False ga4gh:VA.8ofjTa3iH-UsklG3Pd7GJy3k_ElrOXp8 +610 MTOR A2034V protein True ga4gh:VA.X0LGdgbZU0Hr96Gt3MD4VceKyZ1QVhMx +3147 NTRK2 A203T protein False ga4gh:VA.4qGAwUsu-KwYzy3TtC-BHfxkp9iTVhED +1169 ATM A2062V protein True ga4gh:VA.B-N74kl0YKd72j1SKQ-kIyRXC2r35bC3 +1522 CDKN2A A20P protein False ga4gh:VA.7XvepTQbGSfOTRnefHNWDQf5RaWu2eJI +258 MTHFR A222V protein True ga4gh:VA.Nq7ozfH2X6m1PGr_n38E-F0NZ7I9UASP +1171 ATM A2274T protein False ga4gh:VA.gIJfW_7dlR6B5afFaIOYrgP6pVgNze8n +1217 ERBB3 A232V protein False ga4gh:VA.M1gG2BIosOTU_zK5CO2Ap9pF7l0TYP08 +3708 AR A234T protein False ga4gh:VA.f8s2ylFw4f-pjAeo6X7NciGDXzAj1Dij +1050 TP53 A276V protein True ga4gh:VA.Gpm_9ttxiaOtJeSZ8R9n4-VGspGDbwyM +996 EGFR A289V protein True ga4gh:VA.OCSj2RbmQzo9e4Ye-LhUlOAZcCDx_Uan +4402 CDH1 A298T protein False ga4gh:VA.0jLKFyHb8pCQyQkPvp-dk_nsa0oMSyna +4126 TP53 A347G protein False ga4gh:VA.9FneVA5Px_EZNkTkJIZJhPtrJZc0ysE4 +4023 FGFR3 A391E protein True ga4gh:VA.Be6jz5hhF6EeWT7Rs_Qme2lhO-HKshgY +752 MLH1 A424T protein True ga4gh:VA.W_Kli2y0K1-qve7xAnxMVR1bSq2MoFQl +1588 SMO A459V protein False ga4gh:VA.zNpkrf-wguogb1O50FENEos0vLFKH5sI +4248 PTPN11 A461T protein False ga4gh:VA.wx-86-OHszlfkBML8tlHYgvqT61wbs29 +1558 KIT A502_Y503insAY protein True ga4gh:VA.olQlqPRCvGFT0RaRtR3e0OxsTyK3Bn2X +3173 NC_000003.11:g.10183681C>G genomic False ga4gh:VA.Be9wEBoLX0OR-TYHUmsAImCIvYaUf-aS +771 NC_000003.11:g.10183695_10183696insG genomic True ga4gh:VA.BklkEp8Zh0pjd11L35qK2LM_RIQuQjuE +793 NC_000003.11:g.10183695_10183696insA genomic True ga4gh:VA.4w5CwZ1ULbKGOAs-RHq_d9qHmYEWzwiN +1785 NC_000003.11:g.10183697_10183698insA genomic True ga4gh:VA.fHzYSOUsT9MkPVTtOLRnrg9mPlv2kZxe +2826 BRAF A598V protein True ga4gh:VA.FG7NG_exMbTIoE5eIXV3Ex7Jl2dqgBW0 +1646 POLE4 A59E protein False ga4gh:VA.ZZtu6dgorD1zRPmdCdaw2ymccNV3Soew +760 MLH1 A681V protein True ga4gh:VA.pzxB4VRFsjgHoroll87cpAyeIH5UIlzz +4415 EZH2 A682G protein True ga4gh:VA.BMvnGn1upgP_4DhUZzqq7nTrBZeGwlgM +4414 EZH2 A692V protein True ga4gh:VA.Qq2lhXzzh2dgOuFIxSmG3N7gqd2JMPjI +2255 EGFR A702S protein False ga4gh:VA.d-cxRxmdXwWFYitodJv5pUwCSXJjg4l4 +1198 BRAF A728V protein True ga4gh:VA.SuO70FPDKaaDpBCZDB6XjqTsIKosRn6v +2332 EGFR A750T protein False ga4gh:VA.e_HKuW34L3NzrQ2wGpLxxf-ZGLiM_nk3 +1515 EGFR A763_Y764insFQEA protein True ga4gh:VA.EfMe4OdFA6TdH5z2BJqw9FYbunT4Cc8r +2658 ERBB2 A775_G776insYVMA protein False ga4gh:VA.WZoe_9hh3suUX99onvdwj3DN2wIO8ISr +3591 RIT1 A77P protein False ga4gh:VA._t7gNoPRmYO2txG5WxJRGAiGi89eZO8l +3592 RIT1 A77S protein False ga4gh:VA.a7MlCx-oNN6TU1YB40YeiTQL6ivIbb7V +990 KIT A829P protein True ga4gh:VA.bvVMze5vjQBOGLCVr3QIBZBPrgstf7pJ +4127 TP53 A83E protein False ga4gh:VA.8duvSyEvWeNdBO63z7JK5Z7WbJDaY_Ql +1474 EGFR A859T protein False ga4gh:VA.63UxIAJhoTDCtktztT2dvGiD9jOcTL2R +1187 EGFR A864T protein True ga4gh:VA.9-a1OO1GOk2gy_LwyoT_kCgheruLeTd2 +3751 ARHGAP35 A865_L870delinsV protein False ga4gh:VA.K18XETTAbaQt1bXu2M9x4U-n4U4gid7W +4129 TP53 A86E protein False ga4gh:VA.lsplWud8RGraTfpnioT-1awdGSS7hbTG +4128 TP53 A86T protein False ga4gh:VA.oOPQ-YTHLVHNA11PxTOycHXVjOKW1BBt +2939 PRPS1 A87T protein True ga4gh:VA.kPRN_KWVtSPrjJ8ZwN-i41xClXP8H7CY +153 FOXP1 AMPLIFICATION protein True ga4gh:CX.AHpMpNc-8ZgQ7kAc8Y5i6Tv49Z1bNb9F +154 REL AMPLIFICATION protein True ga4gh:CX.m4VdGI4fjws1u3AfMy122CzHadsu78bU +204 NCOA3 AMPLIFICATION protein True ga4gh:CX._8O30NigYzMIAx7b5CZNIEh0dEwtqQKQ +224 TTF1 AMPLIFICATION protein True ga4gh:CX.2NXqgeS6-ezw4PIzqGS6_iM5Mq5dR9r5 +2655 MYB AMPLIFICATION protein True ga4gh:CX.pMO1_7j-ZzdZKLl7A-FnnpnOP3Emt15g +18 CCND1 Amplification protein True ga4gh:CX.juMpRJTQe-cXd5NwCZLkW4rYlSF3Wy0r +180 AURKA Amplification protein True ga4gh:CX.uLiJZi49tL7UJtcC8qmt0dXigJLG17AW +187 CCNE1 Amplification protein True ga4gh:CX.V9Dwgo088Y2XOdhS1NYQgsMFj48ApJKb +190 EGFR Amplification protein True ga4gh:CX.sEHT64Lm86QaTXzw39uKLkBUbEkp4h_X +212 PIK3CA Amplification protein True ga4gh:CX.lLfUpR9E3ehVCteToRHhWUuRiePR0I7e +219 TERT Amplification protein True ga4gh:CX.L1eDe3_dgmjb0fIca3q6phdS293NE8o0 +251 BIRC7 Amplification protein True ga4gh:CX.Qx3pJfEER6sFjLRZBsul0WivMB5GPOAd +267 FGFR1 Amplification protein True ga4gh:CX.H2AKyhB78TWf738tf7xGCXiqTN35A4fF +270 MET Amplification protein True ga4gh:CX.yUMibVYKc6dUxE982VhjXK-exeJydtQh +298 MYCN Amplification protein True ga4gh:CX.gHAyf19MR2VI1TmLuVrbxdYfGJ0doM5a +306 ERBB2 Amplification protein True ga4gh:CX.sfdL4tI7NYIKXtcL2jJyo3tzeoeYOOcS +321 MAPK1 Amplification protein True ga4gh:CX.NCGpFWP0XfNoHqCQz-UA5s-6t06gCGds +330 NOTCH1 Amplification protein True ga4gh:CX.VgbWGt7U_AlFgVIUCv-qeX-AV9-sYKy0 +358 RSF1 Amplification protein True ga4gh:CX.hllVHnW8DnMfkP83DD7LaQeP1ga59mDT +371 TOP1 Amplification protein True ga4gh:CX.p37yoDxWYByrm6N4f_uL2DP0DEitXSAw +379 TYMS Amplification protein True ga4gh:CX.WpxFSk1V6wlwfRUpevPfnCNfQ3oW8Tb9 +407 ABCC3 Amplification protein True ga4gh:CX.qE9DgcoD6hYHs3cfptHM-lb1wm1eOzIx +409 ASNS Amplification protein True ga4gh:CX.67v8cO56x1hmNG6tgpLAid3MA0Ysst9Z +553 CDK4 Amplification protein True ga4gh:CX.ms7wmVsTZc_x0cpgfDQFvplp8ptIHBH9 +573 RICTOR Amplification protein True ga4gh:CX.mJxC4vNmGPYUMXaZIYkYe7UYROnjEtNx +586 KIT Amplification protein True ga4gh:CX.TEy03PVyUmjHBTxanGyWzVMp20MHyio2 +591 RAF1 Amplification protein True ga4gh:CX.SCyuIFMpMiET5JTP3rfm9283MLyXJBwX +592 KRAS Amplification protein True ga4gh:CX.sMK39pbILvGTUFa7plt0m-uQLD6Uvw8q +629 FGFR2 Amplification protein True ga4gh:CX.cd2wF23PpDn8-Y3HxFAhYi4hRBkxrx7e +630 FGF3 Amplification protein True ga4gh:CX.pqDTNc9SDtT1eDSgNrFvukuSOb7sQ1mq +635 AKT2 Amplification protein True ga4gh:CX.ejM5hrpAt8JgLrAZTvoEcHQrsqotnKgC +716 PDGFRA Amplification protein True ga4gh:CX.djhRFuSjFfI6vLoBQjIPD4krb7Unxkvu +1261 MDM2 Amplification protein False ga4gh:CX.pVj4Qo53bz9VqFkyHuzH-MdahZnLwKIG +1268 MDM4 Amplification protein False ga4gh:CX.y3GiaJOHiMDkZqKSxE3X4USW2VXBfQFC +1269 BRAF Amplification protein True ga4gh:CX.TZBOQe5xFojvFJ1XjQQD0633rStHtGUs +1276 SMO Amplification protein False ga4gh:CX.zAh4VLKQn3RsYV-UZq0fDOOTc2oSPy0i +1280 NTRK1 Amplification protein True ga4gh:CX.b-qTv-0a57a_3ei_V0fB56ykAbXeomWS +1281 NTRK3 Amplification protein True ga4gh:CX.s0QOSMBZ04I05yVl-aMYCGXHba07l_tz +1684 PSMD4 Amplification protein False ga4gh:CX.vqx816n7HsN1QpL9Y208v3jpOMUfJqKj +1685 CDK6 Amplification protein False ga4gh:CX.WthC_1sK9xeQv9PNRrPORPPvSuiavs5L +2205 FLT4 Amplification protein False ga4gh:CX.xIhBNM8wWn6eqGZq7_9ZHNZdg1JITxcL +2240 TLK2 Amplification protein True ga4gh:CX.LgutMoXJbfaZ2VtOnAiheOS-Atja2rLM +2397 CRKL Amplification protein False ga4gh:CX.co0a3VJT3K1f2Yo9PV_45vJfCM9j22p9 +2550 NRAS Amplification protein False ga4gh:CX.J6gxXcgeINUTaNYpJqLXqqgt6Qj6cuui +2564 MYC Amplification protein False ga4gh:CX.dtGMpye8n2iy2Ly5SzUrzguxuVtflgST +2598 IRS2 Amplification protein False ga4gh:CX.DvdKyqqC30_F2Fvq8IWC0WdIbyzSGqDz +2619 FLT3 Amplification protein False ga4gh:CX.sovvZfqJupfDZ2whLd9OmNGQPZrfBaBV +2637 KDR Amplification protein False ga4gh:CX._xjVdkReb5SjrGhwTMrUNqKLl1-34rX1 +2746 CCND2 Amplification protein False ga4gh:CX.78Cd1pWrX9oFX8NQrNnmlvmyBP_PynoC +2747 CCND3 Amplification protein False ga4gh:CX.snGEICIn_4wNAikMj_UUXrWz-JZaIMAj +2844 MITF Amplification protein False ga4gh:CX.fNN3I8xTtuDxPIzCY5KQ6z6ciECvyXTg +2906 FGFR3 Amplification protein False ga4gh:CX.MgSZeG9hUFQlV6Ui--Z4Ctv-WsD5SFDV +2907 FGFR4 Amplification protein False ga4gh:CX.Fa30JZmQ88unhirCQzCDMlkqUBTysZC4 +3687 KMT2A Amplification protein False ga4gh:CX.nRwzafgum8uToaCFHPi42uTYx_P3d5gI +4301 ALK Amplification protein True ga4gh:CX.Q0E3OdIAa1WwVmD9ZOEXsuYhfiq_pFF1 +4423 TBXT Amplification protein False ga4gh:CX.-mRkiBlkMgyAT9hpHT6yBYBp5t9UMn98 +4331 ALK C1156Y protein True ga4gh:VA.2Xel_XFk_LNPviJvx1JG4DJDXLq2QZQ_ +627 MAP2K1 C121S protein True ga4gh:VA.wjBDXOXnaZTkYjuhTe0Ey9RQIVS6XIfh +4113 TP53 C124R protein True ga4gh:VA.-fj88HgDE0zrYYKp34ku9KR25p50eQhM +3547 PTEN C124S protein False ga4gh:VA.EuITIdcxvt5caGyky4_ESuW66ZJPnREl +2840 MAP2K2 C125S protein False ga4gh:VA.3FJAVMDQER102O63YdI0slP411xIN9Fc +198 FOXL2 C134W protein True ga4gh:VA.F2H4sYDjFZw0JIU1-JRGIkx7wUWIfUNG +2719 TP53 C135F protein False ga4gh:VA.Jubii9lYZRd751Id1nwCSwqRmLIU2PXu +924 TP53 C135W protein True ga4gh:VA.PhCF9WC4XCR938phjedVf7cV4r3sBO9Y +1111 TP53 C135Y protein False ga4gh:VA.uuAna9GXnZrJI2JYyVrYFK4_3vaQTRp5 +3382 PTEN C136R protein True ga4gh:VA.ZqKaQuEgerygfsh-tsF64Jus5DGeRJuW +1094 TP53 C141W protein False ga4gh:VA.9hVjOVlTTnpyLyhDJtfWvLZxadMj1XYP +2713 MTOR C1483F protein False ga4gh:VA.nu0LZn-UUNCAAS_-so5p7LCutTC03jdY +3413 MTOR C1483R protein False ga4gh:VA.9B-0LLrAIYaUNHcOsYq9VkzFLp8FAoSt +543 MTOR C1483Y protein True ga4gh:VA.UH1nCST9aqppuuQhTDg6WauuRRJW6zP0 +2528 NC_000003.11:g.10191493C>A genomic False ga4gh:VA.pK2T6r2GD6nQ3IKpm0ZVhRAzveUuiHQr +1773 NC_000003.11:g.10191492G>T genomic True ga4gh:VA.LUdpe2nmZN9P_BvG65L1E2ekxSeAmm_- +1772 NC_000003.11:g.10191491T>C genomic True ga4gh:VA.EZqrWOvvzbYx-Nx7TUfq13pHlazUBfSW +1774 NC_000003.11:g.10191493C>G genomic True ga4gh:VA.cetWpHgSIVbXpzwgAWMnM_tmjg-nLeQy +1824 NC_000003.11:g.10191492G>A genomic True ga4gh:VA.yRvo1lHWLj4G29DtT3wb7m47K8t7F20M +2035 NC_000003.11:g.10191490del genomic True ga4gh:VA.KdoESNewkbqKezEK2miNKFGs91oq7zYY +3389 TP53 C176F protein False ga4gh:VA.G2NfEk7zDG-pPPEptGzqgstP6tEZy5v8 +4118 TP53 C176S protein False ga4gh:VA.6rpT6y0yLiP0qWEjfOrAFYRIln8dEhUl +1116 TP53 C176Y protein False ga4gh:VA.SAjjxg5DEsMs8_pza3WzsjQLTBOGMHmH +3393 TP53 C238F protein False ga4gh:VA.nl_YEhghke9GSyB2CnbRWFIayY2Q76o2 +2648 TP53 C238Y protein True ga4gh:VA.YdfpUvm3aP2l-i7JZn2sA48aEz8yhAp5 +1062 TP53 C242F protein False ga4gh:VA.L_fSO_mqiOPhgqRrBxuCpx6DKMVFYLxI +1063 TP53 C242S protein False ga4gh:VA.W8NoZwHkHDOnibLKOnlU-hPrLIWE5m6G +1064 TP53 C242Y protein True ga4gh:VA.PwOLxoho01hPsf11mD3Rg1MnAUYWTVRF +1172 ATM C2488Y protein True ga4gh:VA.t7CnkVy26VRGpLsS7s47dNMgfs4OHtJq +4124 TP53 C275F protein False ga4gh:VA.K8tJPCy16splNpp0ZqH9RVHIyHT8hiCc +917 TP53 C275Y protein False ga4gh:VA.aaUFAr97guheGKpZJdNg3sRmPlPkr3Pv +4145 TP53 C277Y protein False ga4gh:VA.pfDkrMkx-7Msg0__EBf_xfs2kglHFlAW +1647 POLD1 C284Y protein True ga4gh:VA.wQvL2ooyWJM9oocuKmN7f96Jkhhy7Gdh +3357 FGFR2 C342R protein False ga4gh:VA.0fLn-9V2YTsDPi9phglv5kwInUvSh4De +3358 FGFR2 C342Y protein False ga4gh:VA.YkCQyHM-r-DsP9TVNVujdtyxttfKWcsv +931 PIK3CA C420R protein True ga4gh:VA.Nxz0N4ov2iqketOQz74Sipp8LgXVyoux +1586 SMO C469Y protein False ga4gh:VA.QFZQXKymISlg-RtkvKwgf_HhV38M9CWI +1639 ABL1 C475V protein True ga4gh:VA.hgRGSE_zK1IpthSvYZrcINLf9bixxW2e +4017 BTK C481R protein False ga4gh:VA.HVeVL0gXoK1bwpsD3fhgm5EJuG3JKi-z +168 BTK C481S protein True ga4gh:VA.AHcxwFro_b-8WCWUUJ-LnjwEwAS_qFRR +4016 BTK C481Y protein False ga4gh:VA.Mj5zOGDBZ8riV2cgdsVbD1dabcq872du +3605 EZH2 C576W protein False ga4gh:VA.QjlqvpDrlLQRVUU-b_yD_qq6XoKLgkji +3337 PIK3CA C604R protein False ga4gh:VA.GaHsDbJOwze7E7JZG0D-JXD3oZoLhzJQ +1260 RET C609Y protein True ga4gh:VA.JllMYd8UWGZJ0X0IH3Hx5qG8xWD6zsoU +1700 RET C634R protein False ga4gh:VA.VX1C3S5rPE65odB9qQ040Q_Ze99a4BdY +112 RET C634W protein True ga4gh:VA.XMXI-ShFVRwoB21HSyk31GLojlTEYB2z +2936 PRPS1 C77S protein True ga4gh:VA.f9nSELnfkTlUAVvPnsCIFV9leSOi-3OS +3096 NC_000003.12:g.10142077_10142078insTCT genomic True ga4gh:VA.ydTRqCktlatSGaX6devzG-cfuoieZe-j +2123 NC_000003.11:g.10183760_10183762del genomic False ga4gh:VA.-d2yTCI6slZ0ttCz_ArpRTuZ9OSnaiU0 +3003 EGFR C797G protein False ga4gh:VA.B6VZmlOEamEtWFmbVwck9GeflaLk0W9C +415 EGFR C797S protein True ga4gh:VA.ZHfUk6LQ6H9mlgPUj8wDeTHZxxtuRkI2 +1574 EGFR C797Y protein True ga4gh:VA.ltgBz4-9__mVPfapbaQIvX0nleoU69MH +1264 KIT C809G protein True ga4gh:VA.1AY_LXLnQJRJWiRHc_dEfByD6PdXn-rq +3756 BAP1 C91S protein False ga4gh:VA.cHqi2G86x2JTgL3_YhhjbCKX8Dtr9pkE +2789 PIK3CA C971R protein False ga4gh:VA.7Oo0FAtK5Riv5ztA7te0_8NennBdFdDU +1660 MET D1010H protein False ga4gh:VA.iVTwfkZ3jCXz2-BNI-EDkcjd38AJxLWr +1651 MET D1010N protein False ga4gh:VA.kSfBi4q3-zUKxksG3IQ4JCOWIBMhfv5R +1649 MET D1010Y protein False ga4gh:VA.rT-kMyOdYh2V2FiQ83niPlj1zxboJjHo +3062 BCL2 D103E protein False ga4gh:VA.Rzx7lZ3mr_5KP9PObsQiusKBCFif64a- +3061 BCL2 D103V protein False ga4gh:VA.5JOT79GPi8SK5D9ZTIN40fYhRGvkwZxs +3058 BCL2 D103Y protein False ga4gh:VA.eFxOQvqBiJOPZnthXOhqvmQ1jbOgxfHB +3380 CDKN2A D108H protein False ga4gh:VA.HeXjS4EH_uVw0oC5EeP-fZLArwTePn2v +3288 CDKN2A D108N protein False ga4gh:VA._BCHtFnck-Erbm9Xy5UKOHv3SID_5E8l +2791 CDKN2A D108Y protein False ga4gh:VA.gznKJxpP4H_PKO0Li0Hpd9mgJhbhYgao +4015 PLCG2 D1140E protein False ga4gh:VA.1cRYRRcFmvFZR0dlJKbxAMPerRC5aa7x +1813 NC_000003.11:g.10188219A>G genomic True ga4gh:VA.J7udzQ0gYLqQJ5zFrX5He-CcqK7lLtFE +2154 NC_000003.11:g.10188218G>C genomic False ga4gh:VA.flcjMZpvHswRwAWPrl2AQgt5gTy7LQG4 +2446 NC_000003.11:g.10188218delG genomic False ga4gh:VA.q5Nw4e4jIGvvBG1WT5KEmMc-S1-ZleDs +3133 3-10188218-G-A genomic False ga4gh:VA.SLkXLheUR-ve173FoEbI1_0Pay64aM7G +649 MET D1228N protein True ga4gh:VA.2l1B1FHypzP4IY1Mi3NofkBeENuAwGVn +798 MET D1228V protein True ga4gh:VA.0FMKIgklL5eehaIvidwnb9I5pJbcin5a +2554 NC_000003.11:g.10188234A>G genomic False ga4gh:VA.0OZfcOiWgtT0Iql9r5y6PKSVCGHuv-pi +2533 NC_000003.11:g.10188233G>A genomic False ga4gh:VA.CPEPO8t4AIMWPMGOM0KexFY6IUvgViWY +2053 NC_000003.11:g.10188233G>T genomic False ga4gh:VA.hfu6NXRDAj6QUVKql3t7K4xBBIbbzhd6 +2935 PRPS1 D139G protein True ga4gh:VA.PA66RFK5j8WgYI1CrMHkBRp4GTXlklLW +3349 SPOP D140G protein False ga4gh:VA.xPlVXm5NUdo-IqJ4AmsI_7_8vZcBZIPC +3040 3-10188286-C-T genomic False ga4gh:VA.ev3x1Y-3Q6yymG55NMrWduPrKR4C9XVK +3553 PTEN D162G protein False ga4gh:VA.HI6zyp8Sg4CEPyDxAxl7aiL2o4uDow8a +135 NOTCH1 D1642H protein True ga4gh:VA.IHETa4JCkGwzqNfc7z1jIseeGKvKq7Cv +1168 ATM D1682H protein True ga4gh:VA.ASu-KJouLG8k1N6jkBkw9xZ9raM0Vt0X +2196 DICER1 D1709E protein True ga4gh:VA.7bwdQh-ZnJn5Lu6Pt7VeMC2DcGancLGN +2195 DICER1 D1709G protein True ga4gh:VA.pwcS7ZAaGlZZ7So4YNAAPhPM9FfTS_VK +2051 DICER1 D1709N protein True ga4gh:VA.c8i9ykuN3iB793XwvINoymBLm_ih2-2H +3802 TSC2 D1734E protein False ga4gh:VA.4li3enojSwGO4Q5GOQkJzcGCK5uqwjNK +3980 BRCA1 D1739G protein False ga4gh:VA.Vrc8L3KSGbL55nPqjPbkhHJRroMuAIGO +3981 BRCA1 D1739V protein False ga4gh:VA.Pnpva17w8nk-dJMK_97L_Ce-leAS9HAY +3123 NC_000003.11:g.10191542G>A genomic False ga4gh:VA.E8QrOZe-47Y7YBu2tj2vhnlTrgMVglJU +2197 DICER1 D1810H protein False ga4gh:VA.UJXQAFSeK7nZTpj_-6c4Hn00msHILycd +2199 DICER1 D1810N protein False ga4gh:VA.oTAukfE3Mvfg4Hf2YrJq6pz21NDP_PFm +2198 DICER1 D1810Y protein False ga4gh:VA.hVdiTSG35ACNXccYSd1GV5MsenFcy_i_ +2920 PRPS1 D183E protein True ga4gh:VA.6aNsvLAXdtoA1Q0e1cM4Mh0fu4U2ko1c +2933 PRPS1 D183H protein False ga4gh:VA.uscCK4yIpq5i8P7Y2dWbBMVJYL9twsSS +2579 NC_000007.13:g.50450370del genomic False ga4gh:VA.w09KbYQad1r26u_zBoORFGXJ-Q2Yjv5P +1160 ATM D1930V protein True ga4gh:VA.7CV5NtqzoziuPEjMqpfHdwHKScTZxgbG +634 STK11 D194E protein True ga4gh:VA.YGyl9PfN0hagZhv-z7uHUsvIuysD2Uds +2141 NC_000003.11:g.10191596del genomic True ga4gh:VA.bnZFTaTFcnGuT_e6iPrqXqdnYCEEDh6Z +2105 NC_000003.11:g.10191596G>A genomic False ga4gh:VA._Nlh1BS_9Qs1Y5s6S0JNPEUfD2njbw4d +806 RUNX1 D198Y protein True ga4gh:VA.bZnbA3YVkt3P-W56tv35nMJIryl7FF0i +2126 NC_000003.11:g.10191599_10191600del genomic False ga4gh:VA.L35K-5pPF8lW5ozNUX6dYOshjBAxmuwe +1641 ROS1 D2033N protein False ga4gh:VA.6XCHxgNSYMnO_8C49TUj0YLj-k_uqawI +3401 TP53 D259V protein True ga4gh:VA.CT96giqRC_ixWTdzV395TQd8RjkmJGiR +3610 BRCA2 D2611G protein False ga4gh:VA.ilwNrjQ9gt-IGEflIQKb0XQLYLcwnj1P +3625 BRCA2 D2723A protein False ga4gh:VA.SSus2cvCeRtmOcWkWursTfgPkUjYwFHE +3631 BRCA2 D2723G protein False ga4gh:VA.gmiv29MfALh4lFQh_KDIgHeyYX8tEACJ +3639 BRCA2 D2723H protein False ga4gh:VA.XV1HxXlfbbVKxGm7hE5y3bnjac3zbNDk +1044 TP53 D281E protein True ga4gh:VA.S5rfwzP4NxorVtu0jFsvrkCzf6B3ADta +1045 TP53 D281G protein False ga4gh:VA.E8RsnH16cZuosZjt81lKU9lNaU68wpXr +3792 TP53 D281N protein True ga4gh:VA._8xfbpkjqRqKwh0teNhbc7yntPLWABs6 +4146 TP53 D281Y protein False ga4gh:VA.vr8Qm0kEw_czTnMGa9lk668fT63m7aiK +3495 ERBB3 D297Y protein False ga4gh:VA.k7QMj__KH44Mhpj-3CJJ9-LzsMdq-Ij- +650 CASP8 D302H protein True ga4gh:VA.e_dsBZj6pT95m21Gxn7rrjgxoY6zg3YM +3611 BRCA2 D3073G protein False ga4gh:VA.ITaKKCcXhNBCKBcLqNEhzaiHkhZLxQ8l +661 BRCA2 D3095E protein True ga4gh:VA.SPVrqZ6OEZJ0dJE8BU-ZK9a75yucwWUa +4222 AKT1 D323G protein False ga4gh:VA.xYUFDb1wS-z7mH5KXJwpQZ6j6zbm0d8b +3256 CTNNB1 D32Y protein False ga4gh:VA.pH245Dojly0ldttk1GviPKBoNOhz_hu9 +1653 PIK3CA D350G protein True ga4gh:VA.kQ6ys8aMMiij1yR1oYGUk0oWPvu78-Zb +3338 PIK3CA D350N protein False ga4gh:VA.grtlRAqW2dv9hMpJ11XVb4cqYg5s-uhh +2852 SMAD4 D351H protein False ga4gh:VA.L1t9Ja58A99bsUUyVhaF-gVu9_x_35uR +2995 TP53BP1 D353E protein False ga4gh:VA.yi8jbp2v-S165zUHuFEUjts0HgZ4t7mM +1606 ABL1 D363Y protein False ga4gh:VA.9cyxVfjsWmhDFlhAIlfQIs1YuMsJgITt +240 NT5C2 D407A protein True ga4gh:VA.WFe6ldH7t9oLoQ6NdKKR3EkOw8tVS62b +855 KIT D419del protein False ga4gh:VA.yiG-fBNu1l2Mdr9cm82ldZy6biMSFxgj +2468 PRKCB D427N protein True ga4gh:VA.koKCGeJ12I9o5W7J8NLVmjdmQhuAUPiY +1560 SMO D473G protein False ga4gh:VA.BzzQlSgsKZV89zgtrPcgfUwQgjDwxYIC +299 SMO D473H protein True ga4gh:VA.9XzVlZJuewSE3lqUdaacGDa7xcU7Rm08 +1561 SMO D473Y protein False ga4gh:VA.UowvZktryVwUaqZP2TXQVWjTXRFf4sYI +3959 SMAD4 D493H protein False ga4gh:VA.A9S8uIlKa0FWoyGEkNGhmXG_rXTX7_M6 +2858 SMAD4 D537Y protein False ga4gh:VA.wu2CIuJpVpxD3AaJaWRfLY6uST8BQsYU +47 ESR1 D538G protein True ga4gh:VA.JJKM8I6FRu7gxOOIHq2fhidjt14HhayL +1399 PIK3CA D549N protein False ga4gh:VA.u8PWpJjkKuLsS2OttVtTM0FkfhB52Xy5 +1547 KIT D579_H580insIDPTQLPYD protein False ga4gh:VA.Jlf8mgieivCQgHc4f67b1YJKTxaU1ELH +977 KIT D579del protein True ga4gh:VA.8WuGAOhZxc18ihCk7ZymEKPdF9HKXVbj +4341 FLT3 D593del protein False ga4gh:VA.DlhmuIAt4MqIaGIBJWAaUBd2CO_wiMgM +579 BRAF D594A protein True ga4gh:VA.tR4phP4I2Wn_NlCTcU3yDRoBNkEI6dzD +2799 BRAF D594E protein False ga4gh:VA.W4XDuDp_20-wWgvJ_zLcYBRWRrcGz5h- +611 BRAF D594G protein True ga4gh:VA.fupsfMCvfi9d_s16tmW9QiMmLUw48972 +2832 BRAF D594H protein False ga4gh:VA.vgdaHcL8YHKUwdsZwXSdM1oKBwSim3yZ +2398 BRAF D594K protein True ga4gh:VA.V_mCg87zAvfbwo-MOlFA0NtyScS_xxKw +1107 BRAF D594N protein False ga4gh:VA.7L28cfHbB9xWZmp_ejlxcYApef4AWcZ8 +580 BRAF D594V protein True ga4gh:VA.fvpaKd7uOAnr7wdfylla2_rMlfHirI6l +3698 FGFR3 D617G protein False ga4gh:VA.cs2xYeRVP-FtwwZTtWHWvxjV1yxzu-Cu +2573 PTPN11 D61Y protein False ga4gh:VA.z4mj5la9mvKIMGIszA0fQx-Y9Uya8lRL +468 KDR D717V protein True ga4gh:VA.VJkz-ldBX6Vh1O5b8BpAilGPsM5rVBp8 +1013 EGFR D761N protein False ga4gh:VA.-YZfh8hQeMKbserhKWl39t9F0k6-jOQb +712 EGFR D761Y protein True ga4gh:VA.oF96cu9kLVa0wzDDDkcELp5WZzmk2L70 +35 ERBB2 D769H protein True ga4gh:VA.ERf58cubgnqBlF9BozKA-xaBaxmuWeMs +36 ERBB2 D769Y protein True ga4gh:VA.1wU2dxmXepQkzl6QR3h5QzGseu4H7X9m +1512 EGFR D770_N771insG protein True ga4gh:VA.8KmLNgQ5p5GD1NXZlvfFLz95oIhaLk-X +1514 EGFR D770_N771insGL protein True ga4gh:VA.t_WLqe5efVQlBmdbIBgqIeLRu2rSJDJJ +1566 EGFR D770_N771insGT protein True ga4gh:VA.BtzUfmIdKEV4cu8P9l_icRZG1-rWdK3x +1569 EGFR D770_N771insNPG protein True ga4gh:VA.JM83Bhtwoe54jKL44fTlyJxZCU4grDs5 +1445 EGFR D770_N771insSVD protein True ga4gh:VA.JnPGOcaOahbbrXqe51Vpw2ErQjNLmOhL +2214 EGFR D770delinsGY protein True ga4gh:VA.ZoigdObO3LjtDIY0KwJQQ4iwbtjBYRaM +1559 KIT D816E protein True ga4gh:VA.LwR7QqN3ij-xFwIxgm4ZVR2V3RMCAVlw +4419 KIT D816F protein False ga4gh:VA.93eDubfiBoaJaCZlnpzfgo8-FeuXO5Xm +1402 KIT D816G protein False ga4gh:VA._S5bACB12DEm-UZVNohiNFk-xsuR4G9w +983 KIT D816H protein True ga4gh:VA.vHPfPMGRksMr4zLq-aO7BKHeBS5GoEle +65 KIT D816V protein True ga4gh:VA.QSLb0bR-CRIFfKIENdHhcuUZwW3IS1aP +984 KIT D816Y protein False ga4gh:VA.xtU8-b_vnraG7m7PuRcKddJUwAKb5aXz +1265 KIT D820A protein True ga4gh:VA.ouvbzqcPi2KpnquZ3PR32fFRS2PMxSSo +2736 KIT D820E protein False ga4gh:VA.LwR7QqN3ij-xFwIxgm4ZVR2V3RMCAVlw +1266 KIT D820G protein True ga4gh:VA._S5bACB12DEm-UZVNohiNFk-xsuR4G9w +986 KIT D820Y protein True ga4gh:VA.xtU8-b_vnraG7m7PuRcKddJUwAKb5aXz +1397 FLT3 D835E protein False ga4gh:VA.9oGkGT3UmQvjr9pE8xh4FRTxCcxHSO86 +4340 FLT3 D835G protein False ga4gh:VA.gAcdcgbGX-Id6CiKiZvSA1Q_5ron0Vj9 +612 FLT3 D835H protein True ga4gh:VA.O_8zMzG5fxCRsK7Xt2MKy5wIzjeAHEXZ +3075 FLT3 D835I protein True ga4gh:VA.JIAwdIkcDdqIh8sSUNfGkhzM0t8AwydY +4339 FLT3 D835N protein False ga4gh:VA.aB5CmU7fuLnkCUjpBucJcVeEaBYBB3sl +1302 FLT3 D835V protein True ga4gh:VA.CXafP9kytGUvmedzqeVbmhFKHuCP0m2m +3011 FLT3 D835Y protein True ga4gh:VA.3NG3xklVw8k0CbA8ymG0KiuqXIipqPQY +3167 FLT3 D839A protein False ga4gh:VA.c9oBGKNh7N5k-nMRIrbBrp55_I37a0z- +3160 FLT3 D839G protein False ga4gh:VA.3aldJ7vTdplRvs5LpDKnjPgd7pGWTQot +3169 FLT3 D839H protein False ga4gh:VA.Zght69rBZKOxSZKlfX6rCjtZoYqG1I4T +3168 FLT3 D839N protein False ga4gh:VA.6hBiJMXZ81bd1u1INifr3pEYEGCxbJqx +98 PDGFRA D842I protein True ga4gh:VA.McKiucxzi1aRHyp6NZ3pDU2fZE5NWlVd +99 PDGFRA D842V protein True ga4gh:VA.bjWVYvXPaPbIRAfZvE0Uw_P-i36PGkAz +100 PDGFRA D842Y protein True ga4gh:VA.seM13RYYC26t89sPCVaNvnrdO97vLiag +102 PDGFRA D842_I843delinsVM protein True ga4gh:VA.PZ5s81hXdEGZQKIV6FIyrqtWvEb5wLH6 +1518 PDGFRA D842_M844del protein False ga4gh:VA._UIbK_8GkNbsX7feeAJaIi4Vj3pgFFFq +3374 CDKN2A D84G protein False ga4gh:VA.EUlFpbPzBUbKvPArX7VPatEatL8lHEmT +3334 CDKN2A D84H protein False ga4gh:VA.Uev8EjNdTmUVJnotO1NUEFH6w0xk2Zy8 +3285 CDKN2A D84N protein False ga4gh:VA.mUElWRUcc1Kfuafv3ljKEWITo3fnn4mo +3375 CDKN2A D84V protein False ga4gh:VA.cTGHXQjr52rELqoKs7VriG1czmQWEpsu +3333 CDKN2A D84Y protein False ga4gh:VA.0W6mmbI2KxUMFfstboIKs73Ti4TKA__s +2574 SETBP1 D868N protein False ga4gh:VA.4pM7_VkkVJ2H06gTP9haIh57dOYgD5mT +3538 PTEN D92A protein False ga4gh:VA.LgWHpmPlIKiWcXR8bW4AImgLcW1Iovr9 +3539 PTEN D92E protein False ga4gh:VA.3mUHavU6HBCR1oPgwZw4SUk4ReGGbyL7 +3540 PTEN D92G protein False ga4gh:VA.AagUEsUH24EN-rqzD1ggTp6fD1vIDRhh +2449 NC_000003.11:g.10183806A>G genomic True ga4gh:VA.VNcN_kwp9g97grDxTG3EJ1jX1zsbOZdt +3541 PTEN D92H protein False ga4gh:VA.j6j-A_DFnEyhioLXoBsGmE1cZEsD0vos +3542 PTEN D92V protein False ga4gh:VA.3uVXMsU_BYx-DqR5Z0isNggxWKtSH5Fg +3293 PIK3CA D939G protein False ga4gh:VA.cGiJXcSUqWPXdJAE34tIcSggJ3uP0g5M +2414 MAP2K1 E102_I103delEI protein False ga4gh:VA.HkppnfROMSGq_bVJjuvf657YZc82UsQq +3290 PIK3CB E1051K protein False ga4gh:VA.bq5cTUN4rQ4_EMjQuKlXrc1584a97Vlh +3464 EGFR E114K protein False ga4gh:VA.OGAP3miAoQap3L0eGaOgd4bJOFFLuxxB +566 MAP2K7 E116K protein True ga4gh:VA.4KnyoN5hVKNfq5zwfACB4hO_fKLhvXN7 +4329 ALK E1210K protein False ga4gh:VA.d6pKkEOCORCY31R1ksci4P50AvI7PDLK +1694 NC_000003.11:g.10183567G>C genomic False ga4gh:VA.xnhmV_BIw8eEHTXEpi1MYtuHl7Se2Fi8 +1884 NC_000003.11:g.10188257G>T genomic False ga4gh:VA.8zhoV_138OsUtIsstaviTWggX82L9eAb +2524 NC_000003.12:g.10146575_10146601del genomic False ga4gh:VA.kA7ZwJtmrPY8qdTgylGWI2qxYSUFhhyq +2245 NC_000003.11:g.10191485G>T genomic False ga4gh:VA.gDhxMNgEvlEMfdZQgkaNrLiMwIZQJ6TM +1919 NC_000003.11:g.10191486_10191487delAG genomic True ga4gh:VA.i7BdznfMMl0ufjbqo4u6opewUchRR1Gx +2502 NC_000003.11:g.10191486A>T genomic False ga4gh:VA.0G9H49iEnAyhEF4mw3lQNEXaFgsHzQKo +2098 NC_000003.12:g.10149800del genomic True ga4gh:VA.pW-5aiQCtiOVjAbM6gGYGmX-jf5r3eUi +2527 NC_000003.11:g.10191487delG genomic False ga4gh:VA.q4Qwvr_IjwzfqjHvoB0UwchET18zwSyp +2050 DICER1 E1705K protein True ga4gh:VA.c25APeT6iiRZXHg9WZlInt0NGujl4x2F +1976 NC_000003.11:g.10191524G>T genomic False ga4gh:VA.hKd43x386-LG3ZdHuQGA3XGAlH2MGyHk +544 MTOR E1799K protein True ga4gh:VA.S5g-TVssZB1IKF8cLoAfRwaSIco_ByWz +4 AKT1 E17K protein True ga4gh:VA.ulPeadFf5rMg7tG-WFIvGOPgFBgFBmvm +1227 AKT3 E17K protein True ga4gh:VA.fEfaCqfc8374ZfCXTdPyVUS0i1qxZvgw +3585 TP53 E180K protein False ga4gh:VA.GnRs6t0ISi8GFd7j2QdMDqZbqEApOgh8 +2200 DICER1 E1813G protein False ga4gh:VA.JA8S9p8nH_3amSkbYqkris8UsSngfFAD +2201 DICER1 E1813K protein False ga4gh:VA.w5_33ICSd4J_d-l6SQ6u6Ly7Sh8ZdkPU +2052 DICER1 E1813Q protein True ga4gh:VA._GACvtDX5qQcg54qKtyYOWHwU6PrqJZs +1777 NC_000003.11:g.10191563G>T genomic True ga4gh:VA.QIawO9pdOh-Hfi3JcLeMWx7ACAs-W2TX +1778 NC_000003.11:g.10191563G>A genomic True ga4gh:VA.k9DoC3DSx0_WbR9szY4HlrElrdROzr0b +1829 NC_000003.11:g.10191565_10191567del genomic False ga4gh:VA.pmJPJYvzTJrivNnQ0fi0E96Bbr2HLS7U +1869 NC_000003.11:g.10191572del genomic True ga4gh:VA.JxP0edphu3V7ZyYwkOEeR-yyECNSVjzx +572 MTOR E2014K protein True ga4gh:VA.oIVBHawsOrT7m96ha9dZwPR9EGtbghbo +1626 MAP2K1 E203K protein False ga4gh:VA.c7NZnnPSJRIgIi7fGguU7o7l-qHlYqTI +1162 ATM E2187* protein True ga4gh:VA.8X7oMwXmGVdfW0Eci0um7yAmgZmDXZUc +3780 TP53 E224K protein True ga4gh:VA.coSQTW6drWv0RpZX0OuY3hgz0Tf-dAU9 +4427 MTOR E2419K protein True ga4gh:VA.xjeJvL6DDFqJXYQZiPJV_8O2wcQJgXRS +3 ABL1 E255K protein True ga4gh:VA.sfWAmVm20zWQeAEbuwWohEshCqIg6yzA +1601 ABL1 E258D protein False ga4gh:VA.dqRDFOMUxxqpR2uVsIs6N36KuYDJnzNq +3772 TP53 E258K protein True ga4gh:VA.2bwBOsRFRh8VdnkyKfTmsUX788whZqsT +1552 MAPK1 E278E protein False ga4gh:VA.iNbNd--u_VH3hepd3gwiewt_HqIaiLdv +1603 ABL1 E281K protein False ga4gh:VA.CiQBuy5iLxDcgN7yihtOwu1iIBR0XS2W +1043 TP53 E285K protein False ga4gh:VA.yLm4Ai5YAnzibxfG1vI6GB4TUOyIarjV +3462 TP53 E285V protein False ga4gh:VA.aL-2Qn81Tpa4ePygPK5WOjEpSXCXQUms +915 TP53 E286K protein True ga4gh:VA.ZXxjpn7pVKh74P4HHuPw8SoeWcQKO7J9 +3621 BRCA2 E3002K protein False ga4gh:VA.Fn98_8mbueVrZBpUoy2oM-A_Qy2-EWUm +3496 ERBB4 E317K protein False ga4gh:VA.SKldMphr6Yw-AxwnM4H1kknZOlxXs_IN +320 MAPK1 E322K protein True ga4gh:VA.gd71aR16HOc7-nHLRgykfj7LcOyu6BFA +2853 SMAD4 E330A protein False ga4gh:VA.Ab0d-sWKfF8YAOnVC_VOVShs3JAdDUc5 +3521 SMAD4 E330K protein False ga4gh:VA.OttFGvc8qHGbsFzOCCWB1ibW9Kthxvmx +1648 POLD1 E374K protein True ga4gh:VA.511667wlWBJLj174NNv5W3ZUUXkzr1-K +1674 ESR1 E380Q protein False ga4gh:VA.ZS5ktWrjjdVR28RTuEdpxZ6OxF1mg4-W +691 ERRFI1 E384* protein True ga4gh:VA.SfZhr3jxZr_-mGixUD0HDQwQIoirkBCB +3336 PIK3CA E39K protein False ga4gh:VA.ZmEnLd5VypVPWgKz6Rxmc1T6-ZHqrSNs +4306 KLF5 E419K protein True ga4gh:VA.eAi-bZDBo2dibN7oc_PdmRMZjYuhbSxN +4307 KLF5 E419Q protein True ga4gh:VA.lqJBqv6mBEcFkbTVp7WDzHUWU0ZNUSHy +1619 ABL1 E450A protein False ga4gh:VA.CG8vvPf8YJzVyYOPxG3znW0QnefoRBsl +1496 ABL1 E450G protein False ga4gh:VA.WMg2Y3I9dwCHmcOq0AHqMIREl6-STyRb +1617 ABL1 E450K protein False ga4gh:VA.ETJr55irzkyf_3CHsD_UWgvjuG_wvghg +1620 ABL1 E453V protein False ga4gh:VA.Yqqmu92a1kAaNUBpqrglQ2IBEznfMNZ9 +1621 ABL1 E459G protein False ga4gh:VA.iDbiOtwh8j1w9agGpIOSfxK6ntnIM5ZM +1733 NC_000003.11:g.10183667G>T genomic True ga4gh:VA.knJU9OiOrxWc_9kH0utm8EZQjy6hj54N +3692 FGFR3 E466K protein False ga4gh:VA.x2qv8cc69wDwveRQ8Yef8ge9SlP7ymRG +3343 SPOP E47K protein False ga4gh:VA.9ndNr0HQN3HKMVS13g1ZW9Wq9753jIuB +3682 JAK1 E483D protein False ga4gh:VA.WU8PMWwihtumQks21F8llo9x5cB_hqrb +773 MSH2 E483G protein True ga4gh:VA.kZ-RM6vuIkg6lpYhFaJWH-vQHQPjETDK +3345 SPOP E50K protein False ga4gh:VA.91oNmIAD8dwZApIrjXk9HQetpeEgCfKp +2282 DROSHA E518K protein False ga4gh:VA.i2L3OY0R5LkCskLtfSnARJYTaXIOJign +2466 NC_000003.11:g.10183685G>T genomic False ga4gh:VA._MoETcMtqtx6YSThqqBCo3Cp78Waz6RW +1734 NC_000003.11:g.10183685G>A genomic True ga4gh:VA.ZnEB3UpRV5x9OU5Ll_Nh5742uST8hsbr +103 PIK3CA E542K protein True ga4gh:VA.fH_NA-yLHTsF_P_SRqWYD-SYe8kIP2IX +933 PIK3CA E542Q protein False ga4gh:VA.2OmWkE5p_GQ9GqfWDHXPMsQdUwinH9Ro +882 PIK3CA E545A protein False ga4gh:VA.cHMY4gTf2MB-43xJURhOJNZERiGzvQYH +934 PIK3CA E545D protein False ga4gh:VA.R1KBKRC-bkw7EThjVXgYKYcJkVBxUihR +883 PIK3CA E545G protein True ga4gh:VA.WABk-_bU9ObST0H0eE72hIj0OEpX78eY +104 PIK3CA E545K protein True ga4gh:VA.JtbA5ylDOt1lGLvvYwybn_s_-vLB8cvh +881 PIK3CA E545Q protein True ga4gh:VA.I2EHsdyKa1RU5mQCVuLxQNcqUODKbmaW +884 PIK3CA E545V protein False ga4gh:VA.AxerHCqLroza-aCL6jP39e8TUBWAFc0u +2709 PIK3CA E545X protein False ga4gh:VA.jLAd-V1HgjXNarrqpewo_ctIeL1JSSjP +1736 NC_000003.11:g.10183694G>T genomic True ga4gh:VA.upoI51w19gXy_XYzj0Ie8XxHBebbEe_0 +955 KIT E554D protein False ga4gh:VA.iiST2cntS6boOunk9Mjj0uCrDPp2Os4_ +794 NC_000003.11:g.10183696G>A genomic True ga4gh:VA.zxU7wu51oLleQDvmGkQNnh1k7Cincd1R +764 NC_000003.11:g.10183694_10183695del genomic True ga4gh:VA.hl0cC2GuAJFxPtsvUF1-tTf0WQlrpwm7 +766 NC_000003.11:g.10183694del genomic True ga4gh:VA.DrRAqz1FDw_r2uFVuWFJiui7czIX-dQL +3449 BRAF E585K protein False ga4gh:VA.VBUrmaZiphNIQZCVGmwGlrJ-ox0e_G7U +1631 FLT3 E588_Y589INSKYFYVDFRE protein False ga4gh:VA.TBHuJLRzWsYPxZnp4LjfcoAfXahRUVXZ +4106 TP53 E68G protein True ga4gh:VA.COPWh42EbsUx9hXTYgSKY6iLbof0H3I1 +1834 NC_000003.11:g.10183739G>T genomic True ga4gh:VA.a-q3q7htP7fdDzzdf_SAwmeGYQ9s-5AA +1412 EGFR E709K protein False ga4gh:VA.Z6UYUWm_R_8UjTpnSlQeqaI59TcPIy6p +1413 EGFR E709Q protein False ga4gh:VA.DIBIISRMgiY9XT7fRHpEfoG7kp7rlsnZ +1956 NC_000003.11:g.10183739G>A genomic True ga4gh:VA.SkGlmHTUqonOuznA7hahTtJ_G2trrQ5x +1572 EGFR E734Q protein True ga4gh:VA.FogwJmUvUuPkATviRBrb_1yRs5y8NNXb +724 EGFR E746G protein True ga4gh:VA.nvpnkZPS_NmCalofu2Pnr0KCO0-ogQ8h +1431 EGFR E746K protein False ga4gh:VA.jzX7ddFffgcTd8vmYKwf1bLCQEZcZxD6 +1005 EGFR E746V protein False ga4gh:VA.5h_vj8tUF4CljCFfuhdgUD3vFYY6AuXg +1002 EGFR E746_A750del protein True ga4gh:VA.FC9y0m2Ii3dJi_Mbaoy6cCcA8p3nDTtp +1009 EGFR E746_S752delinsD protein False ga4gh:VA.GBkS6eqm1xNf5ExSwgtYKDsxX4tgRVK7 +4280 EGFR E746_S752insV protein False ga4gh:VA.Yxz16KWwSsgDTmrI7Bs6g02t5DLxJ5ls +1004 EGFR E746_T751delinsA protein False ga4gh:VA.yaecOlROm8HFv6KGmMB7H-VcfpD-hZ8Z +1214 EGFR E746_T751delinsVA protein False ga4gh:VA.fhM4_hCt2_R4zNAYPqJ8H6eEGI8covol +3754 BACH2 E788K protein False ga4gh:VA.etFz6iGOJQA0UPny-qGX-gijMozYfaVD +4476 TET2 E796K protein False ga4gh:VA.Oxx1eqH4xZiEWz1j7P5uYRbe4s00aFfd +3504 ERCC2 E79D protein False ga4gh:VA.ekggXnaZciytlJeS-21FXCROyH4YQzQa +4320 NFE2L2 E79K protein False ga4gh:VA.UQS8oUEeADyTzO2HBHII27qaYXvYlSUg +3960 NFE2L2 E79Q protein False ga4gh:VA.CS2Yj1h9a9J4jLFnnJK8FrW0uJwZrmh3 +1500 PIK3CA E81K protein True ga4gh:VA.HBvAd4zv0mpRyATWOeyueLRq226yaf0c +3430 NFE2L2 E82D protein False ga4gh:VA.ztZe_z5g1ow-sWpMhv-z5pWFjc3-Yt-f +4107 SOS1 E846K protein False ga4gh:VA.r5O7j4MLcwrys-H4xron4VHbYxB0RaC- +1482 EGFR E868G protein True ga4gh:VA.ukHTjNjnmoRi9tDcG2aGX3HJ1xoGtmCi +3505 ERCC2 E86Q protein False ga4gh:VA.G_xuihyzCVqLZ5D9X39AqWo9oGwEnjnp +1390 EGFR E884K protein False ga4gh:VA.nbgLpcqfhlZSxsCK9Dr5Ie_Bm7xIyn9y +3332 CDKN2A E88K protein False ga4gh:VA.LNOHMOodlRsUlCCQAI6h4DCAsyzJdmvL +3537 PTEN E91A protein False ga4gh:VA.KcWdEvcKla7k7AooiViSeRdubrjNlk8x +1794 NC_000003.11:g.10183811G>T genomic True ga4gh:VA.AapTebzo-gKCamjoz_fM5nEWJJt-7F2q +2127 NC_000003.11:g.10183810del genomic True ga4gh:VA.cZhnnTXELhKm9jG9saF2zqkeG6zJwfQG +2173 NC_000003.11:g.10183811G>A genomic False ga4gh:VA.c12lAGBuijr_d9sVnayTvy7yb3_HvATf +1158 ATM F1025L protein True ga4gh:VA.0M2AEzhmmU4-NDY6LvvTGN3S5z4lPicI +3082 BCL2 F104I protein True ga4gh:VA.imG4s_nFYKpBe43u21rT7RNGD5qKye96 +3028 BCL2 F104L protein False ga4gh:VA.Gaxh8SRFtep9by4HnOs2N9mdffFIudpi +3027 BCL2 F104S protein False ga4gh:VA.IGCgD0wqH9Duk7R4ZFWpVxy4LP8E07Og +1492 ALK F1174C protein False ga4gh:VA.QtaGjdrAZEW4sT-7WAwaCwYghSEdhh8s +8 ALK F1174L protein True ga4gh:VA.xnPNIq4LYd_9sTeSwHefhweeHYLwMKZj +1505 ALK F1174V protein False ga4gh:VA.nDVVUNsSbt3kUiCwPVKmG8txlg3z46k4 +2475 NC_000003.11:g.10188212T>C genomic False ga4gh:VA.1CpjjcDAJFIyMwJAbPsu8xDlUnxAVHcI +1743 NC_000003.11:g.10188214C>G genomic True ga4gh:VA.lcoatsJnOywB9PZR8j3RbGpxC5QQosuE +2119 NC_000003.11:g.10188213T>C genomic False ga4gh:VA.wKHarkuDncBLbYwYHuo1bcOhYOpQ8cMC +1945 NC_000003.11:g.10188211_10188212del genomic False ga4gh:VA.hvwBZON5KzQGQazIMpeUu_dmyJ-xN8EV +549 ALK F1245C protein True ga4gh:VA.pzfMOXaBGI9RxlmNAPjjo1Flrl728mGK +1295 ALK F1245V protein True ga4gh:VA.LbtBjrjzBi9EPMokdR4xEGZCRHgrZSe- +1814 NC_000003.11:g.10188264T>G genomic True ga4gh:VA.7EaeYVvUM6GYtmCW7rTGxUwOOA99dcB4 +1801 NC_000003.11:g.10188264T>C genomic True ga4gh:VA.-2oCuXph8B6m1InImCgF_IDjwZtMJh7L +1174 NOTCH1 F1592C protein False ga4gh:VA.qLrs0uxngLJkfmIRcj4-WzUGIQ02Fg08 +1127 NOTCH1 F1592S protein False ga4gh:VA.CiiJiQR21YxjLpkKXIXU1MJ-r0R0tHAn +2714 MTOR F1888L protein False ga4gh:VA.L8WEfqqBBuu6WCWuB6F7Yr2eDJ36J6zm +470 MTOR F2108L protein True ga4gh:VA.p2O6-26KwxseKgMPhD4Nw3I3Gt1uTbIH +2285 CRLF2 F232C protein False ga4gh:VA.PSZW6PWJj_mHgDq4T4dMv_3XJ6wA7Kf2 +2802 BRAF F247L protein False ga4gh:VA.1x78OTay08mFXX8yQ6NNTczlSKmIEyjy +1053 TP53 F270S protein True ga4gh:VA.M6-x2b5ziSEOpmlhFqHA7d0xkhzLJnXh +1164 ATM F2732V protein True ga4gh:VA.JR_me78SMLdTKe7SJVX-i5UDBTMcFlZu +1507 ABL1 F311I protein True ga4gh:VA.7mRMuGUpqmNZaNPN0pGVUS3tZZ5wYE7k +1028 ABL1 F317L protein True ga4gh:VA.KthZ0GvMM8IAq73dQ1Bqh9e8Ys0LKL8p +1525 ABL1 F317V protein True ga4gh:VA.ZQYG0E49jxi2VTHK3Fmfktzg5KBW0is5 +2063 STK11 F354L protein False ga4gh:VA.NfvgOAJgzlcJpyhcFmEfXvFpRuu5VET5 +3516 FGFR3 F384L protein False ga4gh:VA.QcCEMJf4nl7283UhC4Dvat__IwoDiOY9 +2616 EGFR F404I protein False ga4gh:VA.Da8bKwqbEpaNbSumDH--OthenmQc9W7l +2617 EGFR F404V protein False ga4gh:VA.7ZQSqCwZ-Y5Al4EaOzyB9h_PI3W2u590 +1538 ABL1 F486Y protein False ga4gh:VA.V1N0zlYcROd8EPAIgD-LhFD7NsbWzZx3 +3240 KIT F504A protein False ga4gh:VA.5PH1oj-KHSwUoK0XDR-QVmyS4BRR36AK +1270 MAP2K1 F53L protein False ga4gh:VA.uk8CH3ERBT5E40COmLLKIT5MoKM4WyuV +2839 MAP2K1 F53Y protein False ga4gh:VA.qFPrMQEhB70SYCeqhL0KkdGOPOCtuAh7 +4223 AKT1 F55Y protein False ga4gh:VA.FEdPSFNiBUnT5Jqkca8LWiYyG3Z-3BUi +1398 MAP2K2 F57C protein False ga4gh:VA.9l_zGx6Ad7k659n3SN2CMOQbuvhREYnp +1121 BRAF F595L protein False ga4gh:VA.u7-eZimx4Q6YLxJZy48P13JLycc-QYwP +3468 NTRK3 F617L protein True ga4gh:VA.XQWh-bjRiuT3_aZoMng6rxOKd3_zwnUy +3071 FLT3 F691L protein True ga4gh:VA.4_yATGhcl_NWTFAxlYcxqJ5JTHfSzaRO +2587 JAK2 F694L protein True ga4gh:VA.jL1yeIZ3R0NCtWCFpT9WyZfWxRJQW6JH +1749 NC_000003.11:g.10183757T>A genomic False ga4gh:VA.dAYqkGIFv2OW8exHccfA4e8gxU8Dydzx +2107 NC_000003.11:g.10183759C>G genomic False ga4gh:VA.AgyObrciaDUpzCJQIaTKeloRcmdw96eQ +1835 NC_000003.11:g.10183758T>C genomic True ga4gh:VA.O0ncPWgnf7ItLhwvy8KKUCdYN3BgvMfu +2088 NC_000003.11:g.10183758_10183760del genomic True ga4gh:VA.VjyGKwwamrFrLd8ZoY_Wufh7ivUNCCh6 +1926 NC_000003.11:g.10183758_10183760delTCT genomic False ga4gh:VA.VjyGKwwamrFrLd8ZoY_Wufh7ivUNCCh6 +3593 RIT1 F82L protein False ga4gh:VA.Ruy1Iy0ekjPXTf5ifdE0qlfziSHvpvVE +1881 ATM F858L protein False ga4gh:VA.gocSfnxOZBYk8jw9WR4oSkLqmEfRHGN- +175 AR F877L protein True ga4gh:VA.t0LkTqShXUx8dHkWpMaNySfp20l2jWEF +3536 PTEN F90L protein False ga4gh:VA.yF6UO_WYic3OVa0HMbN9eyLG9CFplqGP +2294 NC_000003.11:g.10183804C>G genomic True ga4gh:VA.6GKIV-pwXbT_AynLytb7JGTJF3b8dshv +3667 PIK3CA F930S protein True ga4gh:VA.a1XMKw_7AkS4IS1tHDMvW9cowayymPts +3437 PIK3CA G1007R protein False ga4gh:VA.dDVceq0hVA1iYglzcQxPveELyiJjv6Wc +3026 BCL2 G101A protein False ga4gh:VA.7lS4WPyyS6pkaQpKMPCB7G6M8UkMNFPa +2960 BCL2 G101V protein True ga4gh:VA.DWMnyxQ3Ul5eZXA1OU5FqZKvk06geSRX +1501 PIK3CA G1049A protein False ga4gh:VA.DJvkwupkc3er9_IEH3HVEbvsoMCp3C9C +940 PIK3CA G1049R protein True ga4gh:VA.wodcxMzUiTgouTS4hF7Eds_L-EDI5UaC +939 PIK3CA G1049S protein False ga4gh:VA.zjfgoWCV21ThRUo54z4iBB5djQuJuERi +2293 NC_000003.11:g.10183843C>G genomic True ga4gh:VA.OSiaNSqRU4GuGxphkX2FDT2EHP99zIZo +2043 NC_000003.11:g.10183842G>C genomic True ga4gh:VA.ZDf1jguzG972xxZDL920FCNisZe5nKX0 +2428 NC_000003.11:g.10183842G>T genomic True ga4gh:VA.HteWsh0DQlYyYUJZfiyqTXXZ6jUrgMIl +3341 KRAS G10_A11insG protein True ga4gh:VA.pUdmc-9a5-uDIEqG-B1I7-55Uz4LRQsz +1673 ERBB4 G1109C protein False ga4gh:VA.e0qijMF4Ry8NSxOwJRg4u0Rnfecq5mR8 +2798 ALK G1128A protein False ga4gh:VA._wA1apCQZHAfFm2BBWoKoKcTHG8bmsfS +1797 NC_000003.11:g.10183871G>T genomic True ga4gh:VA.aoro0_eLNxkyI5e4bfF64QGT2Fdi7t-a +1857 NC_000003.11:g.10183871G>C genomic True ga4gh:VA.G_37JsqnnyO8KfqhJdrrrkGzt1Vc_CU6 +2026 NC_000003.11:g.10183871G>A genomic True ga4gh:VA.kRYxPV2ddEZUWaZzHVq5B_DOW6L1Lep0 +2491 NC_000003.11:g.10188198G>T genomic False ga4gh:VA.b0Pj_Vfh0ZnAvgFBMRdRHYkawWVTEfIU +171 ALK G1202R protein True ga4gh:VA.otN-O6TmlrfPGEU-YDDmtdaXLY7zk4Zc +2813 ALK G1202del protein False ga4gh:VA.e5KL9amKep0uMABc8JcPA0Ad8ts5sK5U +308 ALK G1269A protein True ga4gh:VA.FuEnPmOTyaN9jQNc1qML9_A5FT64KZAF +4334 ALK G1269S protein False ga4gh:VA.ckVG-FHf-FhRh9c2g9nBoGninX1UDdwm +3549 PTEN G127E protein False ga4gh:VA.r_qf3FUdeImpAKBKdMFOHOOdjvvm9WIo +2555 NC_000003.11:g.10188238delG genomic False ga4gh:VA.7jIdgftE5dt7X_CJ1pBScZ58SOExiKH9 +2835 MAP2K1 G128V protein False ga4gh:VA.NH_zsgOzk6P4FfYxB7oEko13om_6M-9P +3563 PTEN G129E protein False ga4gh:VA.tS7nQWmQMS_Cok8QB7c_rxt1L2ryUPA8 +3562 PTEN G129R protein False ga4gh:VA.Fo0J44dc3TFCMQSiGXlF_EvyI1GE4LNj +3561 PTEN G129V protein False ga4gh:VA.qzMFq-9dmwS0FLgsRghB5W8r1Oc7MFOd +148 KRAS G12A protein True ga4gh:VA.lJHBFaaEWU7F0gKG36Nt4pXpDCxngcMq +78 KRAS G12C protein True ga4gh:VA.GtaY-fkmnMXM-bRKyu5qvya6Zd47AM_X +897 NRAS G12C protein True ga4gh:VA.gb0-lfGQqY52tTY-gQNkpQk_-kjOUMBh +79 KRAS G12D protein True ga4gh:VA.NtQTqsdO_Z8G0KpBQ1_z7QsHo_bVN43m +878 NRAS G12D protein True ga4gh:VA.6fySa8P47Q7DjsqrGKMSKS2fYpzdZdl3 +1387 HRAS G12D protein False ga4gh:VA.w7OzrFHsRE7KePmoZ2t4i1GKotJ_M8Rn +530 KRAS G12R protein True ga4gh:VA.XrtQMbIWvN4jWw3I-xLU7aTZvdXrAzIj +898 NRAS G12S protein False ga4gh:VA.DJ3mHANAwaWBHoP_tlAABMVJOpbi43Wt +913 KRAS G12S protein True ga4gh:VA.FJGn9KCoGagWFJC0FMqdfErve-qLv32d +425 KRAS G12V protein True ga4gh:VA.Q9M7w7IYlef17H0ttlmVxuvf4OYNNE2n +1175 NRAS G12V protein False ga4gh:VA.5Jmah15DhleqR_L4Cceck2zoYY4UAckz +1394 HRAS G12V protein False ga4gh:VA.E4qw-Y5ByIfQqdI6hUSmeeNzfxQg96JB +2873 MAP2K2 G132D protein False ga4gh:VA.lCvq-SQ8zWxncuHnfMO5pdhNQ6VRbiTM +2874 MAP2K2 G132S protein False ga4gh:VA.aXMytYaD50rxvfdr5hhI7v1bKcgGqXKo +895 NRAS G13C protein False ga4gh:VA.ESmUKTTQBHLH6BR6SMIg7OW4JSSbpPz6 +911 KRAS G13C protein False ga4gh:VA.tkhm3fgqtGvVZEk7aZdpyHXM3EsovwyB +81 KRAS G13D protein True ga4gh:VA.pwrJYMofSZkG6D9DtJRUYHGDhrJw6Liu +93 NRAS G13D protein True ga4gh:VA.Vi9_O1D0NZjlJHY1C8iErs1ulF2NLy0f +274 HRAS G13D protein True ga4gh:VA.0VN_pxGDVysGaN0IeAfxbLmdunW-4r_n +896 NRAS G13R protein True ga4gh:VA.4tkCjhl90tVBA3W8-4kPbKjOp82X16yp +1393 HRAS G13R protein False ga4gh:VA.rUt5eVm5ZMLO9TaBQRWF7xy94yXU4YFU +1395 KRAS G13R protein False ga4gh:VA.99yKRG5aCkFXZoEiVZz2VPXITKT5MZwS +1396 KRAS G13S protein False ga4gh:VA.wwfrruyQO7rBTf5dvm2udcz6f2mKHtDp +1317 NRAS G13V protein False ga4gh:VA.1_DTGp3bCIrFFYD-jhIYggCZRvhFY9P9 +1489 HRAS G13V protein False ga4gh:VA.nLjiEOSBgDZa5DCQqK0F7wJW-Bcf6igZ +1517 KRAS G13V protein True ga4gh:VA.YmzuS-Jsf_IaeZYJQ4e9S1jeW6M5ZdLI +1850 NC_000003.11:g.10188287G>T genomic True ga4gh:VA.27vRkzJIOJwOJd9SMo2b9oeyS5nbM_5r +2290 3-10188288-G-A genomic True ga4gh:VA.BfgMpTbJ-jcFtw5F0B9KXVDNtXS8u5Zz +2059 NC_000003.11:g.10188287G>A genomic False ga4gh:VA.YdcpBQd9bBHQHdn6j1ZHvXMf1KE2skqP +3197 3-10188287-G-C genomic False ga4gh:VA.7EjrApsBEofnBdv50O8IKvhxgF3WP2Jq +3247 NC_000003.12:g.10146602_10146612del genomic True ga4gh:VA.AdPCDJmmcBg0MlrnkgGaOF_wGGE2XooU +2560 NC_000003.11:g.10188288delG genomic False ga4gh:VA.UGhOwXiJStvinlt6yF0eY4GVCvkr6OoX +2676 EP300 G1506V protein False ga4gh:VA.zl35ORa3gzY4Lm26fpBp6qmIGkMRBpM1 +3419 TP53 G154S protein False ga4gh:VA.9DJKg6juagrCt2VWE9ifgBq4Ao1kWE_h +3559 PTEN G165E protein False ga4gh:VA.F-HcLOEygef4I360hGL6Ig6hrAKjj2Kj +3560 PTEN G165V protein False ga4gh:VA.TwLKkdp-pbx2OaiPGc4wJlo2UXum8LJx +3973 BRCA1 G1706A protein False ga4gh:VA.JVtlv2mTeU4gKqW0i1Hty9Vv5uiHSHKz +3972 BRCA1 G1706E protein False ga4gh:VA.YMv4jfKXoa5ntXGcvsvkGXba0PlAArHU +2922 PRPS1 G174E protein False ga4gh:VA.a9HMj8p6lc98NBjEEBQDNBiNtEasqj76 +3993 BRCA1 G1770V protein False ga4gh:VA.d6VN2b-CMYBzUvkUO3aHxbjS5a3kSmNW +1271 ROS1 G2032R protein True ga4gh:VA.whyduWlc0D-kr4hastmMLMGLo-LjPLWy +1060 TP53 G244S protein True ga4gh:VA._vwANKpqn28h5uJfqGOOOI30mhrHA9Ym +3397 TP53 G244V protein False ga4gh:VA.3ffmuOTWbWWLNfHXiv5z6SYCLkxfez73 +1036 TP53 G245D protein True ga4gh:VA.kvnvir4ELmXlNoDYliFqwQ8rVbuJ4HAv +879 TP53 G245S protein True ga4gh:VA.9vQblQgJFxtYjtBFu89nD9DxzsyzkfWq +3331 LZTR1 G248R protein False ga4gh:VA.MlbVU1fnarTVYuqcY_5tK3_PU9MMaC7Y +2279 CRLF2 G24R protein False ga4gh:VA.C4evCtuAXVtEvSe9u3FTIqLSXYDMZx9N +1599 ABL1 G250V protein False ga4gh:VA.y3KH-nTM-uFkjL8FPMa9srcsCdBGtd5X +3523 SMAD4 G252* protein False ga4gh:VA.86SHaB-L6gOL2M6znZ25nexuWUyj4Bre +141 DDR2 G253C protein True ga4gh:VA.OusOOi6elBACqbc0H_9zV8N1Wol0Zpj- +3615 BRCA2 G2585R protein False ga4gh:VA.O4gGtmqtQkKaun-g-cUblSIWt_untotZ +3628 BRCA2 G2609D protein False ga4gh:VA.g-9jhkiLCa-zv5els-2k50qNOW7G-wOk +4144 TP53 G262C protein False ga4gh:VA.Feef9HFRqbxNNpj6HyakHv21K1jxmuLd +3773 TP53 G262D protein True ga4gh:VA.MTM9ZeLnZjPiOO0iWI80gQPDsnWGI4Q3 +3774 TP53 G266E protein True ga4gh:VA.AzVF_w9EgkKTIFN7BA8WSWxAHMegmyfd +1055 TP53 G266R protein True ga4gh:VA.y4V5fepSgvf9DZRKIIRvyN-q47KtKVs1 +4122 TP53 G266V protein True ga4gh:VA.jWtRcCUlI90M6ovnogZDUIO0YrmAtDXW +2838 MAP2K1 G276W protein False ga4gh:VA.aUhBRb9uyHKDmSnJFk8H-SQN9MZ-9TcP +3613 BRCA2 G2793E protein False ga4gh:VA.Vg9aO5ZXEmVd6ypL-udFDDD6xcUVB12V +3616 BRCA2 G2793R protein False ga4gh:VA.d0yS6G_XplF7gLjOZpNQ8W9WTv06MPg9 +3791 TP53 G279E protein True ga4gh:VA.IlH5tkywvF_eyTz-CTb9VmIKjomsm_wk +703 ERBB3 G284R protein True ga4gh:VA.-lWawk-cmTAFyQcWAQXOL5DoPTYW3zN0 +3623 BRCA2 G3076E protein False ga4gh:VA.ocsmBQddvDzwgfI327-4yfFPWwucBSRp +3620 BRCA2 G3076V protein False ga4gh:VA.20eT6-i-INgGEoDrxVd6F56IU4Ur1UXt +38 ERBB2 G309A protein True ga4gh:VA.DgMOPcxdzFkO30hewV1GmHNfvRGqil0G +3457 NFE2L2 G31A protein True ga4gh:VA.8S_xRZ2nzChkzUBHiibCNog24wpJ4wzX +2283 ACVR1 G328E protein True ga4gh:VA.AGU9eGmZ7DIAxZqSiy-MU0yYlAkt_Nog +1686 ACVR1 G328V protein True ga4gh:VA.yuvNtv-SpNOzcGsKsNnnK0n026rbfp6T +2280 ACVR1 G328W protein True ga4gh:VA.sJ-kE5LD11e2E29Xm--4kcrsP10D-7Av +1657 ABL1 G340L protein True ga4gh:VA._rS70f-PA3wWOZqd8Y00rOvPEn7-1Orb +3492 CTNNB1 G34E protein False ga4gh:VA.t8K2eqmn2YUAgXlku_vpqnLCmg6sKKyz +3253 CTNNB1 G34R protein False ga4gh:VA.Eh5AFuxA8H5mIY0-DBzIruiM28Gy0ugV +3379 H3-3A G34R protein True ga4gh:VA.Q6rl_FhfGeqdUCBlwUvsRmNr-1j3PtG2 +2576 CTNNB1 G34V protein False ga4gh:VA.J4-gTrYQe-Vt4hR9cIHjGONul049aFby +3378 H3-3A G34V protein False ga4gh:VA.v4T9d8jcxO3wjl6MJMom7F3N6JieWKOT +2421 H3-3A G34W protein True ga4gh:VA.IZrqKSRJO-Qdb67-LtGpjd0u5dTp3aqX +3662 ACVR1 G356D protein True ga4gh:VA.Li3yuvmn8Y7Y0ut34L-D3snkiwzhMmPG +2788 PIK3CA G363A protein False ga4gh:VA.E9nrqAwQXg7Zb-DVo4lSbON7kVInza0I +3286 PTEN G36R protein False ga4gh:VA.b33oTVYoApuNROowSRvXTaLxeEHnMEWa +2406 FGFR3 G370C protein True ga4gh:VA.F19w5rQJOPFV5ratrP1qhkNUUEk8l7Ee +3381 PIK3R2 G373R protein True ga4gh:VA.JKFasqqKr0El5SkHArw7IUAp27-_4vgR +2405 FGFR3 G380R protein True ga4gh:VA.1HWZtTkHGPT609tRwn9WcxNeh2jf10SH +3522 SMAD4 G386D protein False ga4gh:VA.DpLBlrjI7Ubqw1KEnZ8ybbJoC9FJZHJj +1737 NC_000003.11:g.10183645del genomic False ga4gh:VA.Cu1wxZpmfQcb4GPcF1DtCeUwve-uqqTn +3520 SMAD4 G419V protein False ga4gh:VA.SpvzR06YnKqq6dO4HdRUBQZGgXfMeRXk +3432 BRAF G463E protein True ga4gh:VA.xDB3lJhWTUBvUhlAsc-5xJgfprh50Ak7 +3442 BRAF G463V protein False ga4gh:VA.VRsDiNc_dD88Bc_tpPu10XH7kSrYWFqV +1106 BRAF G464V protein True ga4gh:VA.xjGc6ZKznSKVGXSVCde8CY5A5SoqDfy0 +2603 EGFR G465E protein False ga4gh:VA.XLZTbEGdFDQ6yINWK8EsFg-PtQsVdD12 +443 EGFR G465R protein True ga4gh:VA.SkqypPvx_rOwQzp6L21NlsP4nq2oVReU +2604 EGFR G465V protein False ga4gh:VA.FzLBqy3_7tGtQV_PqkfXxO3aBIoY4KwP +1196 BRAF G466A protein False ga4gh:VA.qCOd3Lhy_T9q2NgXASCUx2UDfKVyo1XF +2792 BRAF G466E protein False ga4gh:VA.eqJiG-nwpKTDUSHdukV0X8wpnZg74Oy6 +2222 BRAF G466V protein True ga4gh:VA.Drm8EFQcqKCpwgG2nzNVffttwvcJ74eq +992 BRAF G469A protein True ga4gh:VA.ikuZ6LsVYQw-ST38I0AYQ8ieB3Cuvcqh +993 BRAF G469E protein True ga4gh:VA.TKB9z6nqQ2snaRcmYCwk3ICFScN1vOb- +840 BRAF G469R protein False ga4gh:VA.nWpjkS2GczCVOYngnORg_ner9cciIU31 +3425 BRAF G469S protein False ga4gh:VA.ccfn271XScrlXUMOu4LFZkDF-ihK1OFC +841 BRAF G469V protein False ga4gh:VA.MUN-ano4o1XnH2TXloLzDyVvFddzCm6P +2221 BRAF G496A protein True ga4gh:VA.jNEoGw_hkQH5LdQ2WtsnUx7Q9-77i_Uy +1584 SMO G497W protein False ga4gh:VA.pihiFP40De2donFasz4KTtXrMIZgvgQT +142 DDR2 G505S protein True ga4gh:VA.OcDKvUr5tJ4MLsu_LztFSc5nUpwysZft +1624 ABL1 G514S protein False ga4gh:VA.2uUCbBz96ZX6HwTOcNPvqFNe5XY-I9cz +4007 DDX41 G530D protein False ga4gh:VA.Be1pwbUAMP0NMYyib8IqdegR_zuS43tV +1678 FBXW7 G579W protein False ga4gh:VA.t-x2aNw8HXuadDP3dbuO3AzrTpJfSW2r +2823 BRAF G593D protein False ga4gh:VA.rEU2kbgm2LwW-z_t90fIS4wRx5h8CvfN +2690 NTRK1 G595R protein False ga4gh:VA.L3RWSyyM-N9-lserSa4r9XaNOCm5ZZeM +694 BRAF G596C protein True ga4gh:VA.r8xacDEO2FXGp6CKq-GmBhjBtqpvNAeA +1627 BRAF G596R protein True ga4gh:VA.X_sinJYVTue7ouLf8EXefL1SgJG9w6_8 +1650 BRAF G596V protein False ga4gh:VA.qo2SqJcK9_wFxMyvzZoFgD5BBB3qjn4G +997 EGFR G598V protein True ga4gh:VA.auttajs2TqIoqD2vyVojDCXFPdvTqUkV +2223 BRAF G606E protein True ga4gh:VA.eAk30I0bMS0-yCxDUuW0-e3BNQtOzDDZ +2855 NTRK3 G623E protein False ga4gh:VA.IQz-vhwGyc6wrmQkZnUuRX2HemekJFIW +2691 NTRK3 G623R protein False ga4gh:VA.qr0Ze79eTW0Rg1cU3NkSTnpKly1jdmma +3215 FGFR4 G636C protein False ga4gh:VA.Hl944DilLH7-0vwnFnJUxQpBBFgr1Z20 +3699 FGFR3 G637W protein False ga4gh:VA.xaTa1en61l8cvfFudoUBjnrqx66uClGg +3488 EGFR G63R protein False ga4gh:VA.nr37nfdEfbZLbJs714lBn2PM7qDe7U8M +759 MLH1 G65D protein True ga4gh:VA.ZKbWFr6PcdHSeczyJIej9Aik3wIeJ5eX +757 MLH1 G67R protein True ga4gh:VA.mb_MsShBjgdH_z9ixXVw_4kjmzPOyvyW +1692 FGFR3 G691R protein False ga4gh:VA.SqIsyfUQ1ZYMHVGG1qYE6ywFgZhhMJLC +4030 FGFR3 G697C protein False ga4gh:VA.X409fmK9j7M78cCR5PCzpnuucy9A7yar +2817 FLT3 G697R protein False ga4gh:VA.pAtLbtuxAJYVKZICwhkSLQ9z6MF_dCUX +3212 FLT3 G697S protein False ga4gh:VA.JJ2cggzROn8P1kHMXcLfF1GMu9gEIY8Y +999 EGFR G719A protein True ga4gh:VA.sNJ-9xkiEN7UG-Qiaca_h9HmmrzxxKjG +1420 EGFR G719D protein True ga4gh:VA.SXCL9Oazkd8pywgp1Dyuvmb-GVNiTKm3 +134 EGFR G719S protein True ga4gh:VA.zW3Nrt8xyqWLfbqRZVb6HVt2Cpg31xOr +317 EGFR G724S protein True ga4gh:VA.z8NNdeb-yBPfrClZE1SfKMC7xDd1dhhC +3346 SPOP G75R protein False ga4gh:VA.N_zdFYxZw6cQY6txE9L1_bo5Y7u-DI4T +144 DDR2 G774V protein True ga4gh:VA.rqbdGgLKnqrDHU6haLIEBgD5Y1dSbvAX +816 ERBB2 G776L protein True ga4gh:VA.4EyM1FZDC00SJOuAokPfhBJBJczKAnuq +4470 ERBB2 G776V protein False ga4gh:VA.cFb2JM8Q67ECTULNselaseNqWXuBBG1J +3649 KDR G800D protein False ga4gh:VA.MaKqvs9UTWF9aFVHEkxM1V1wbk79c8M8 +3650 KDR G800R protein False ga4gh:VA.waivUswYRuHtdEZagDv-xa3kLpw_vRTY +3226 RET G810C protein False ga4gh:VA.LrRoFWZkq6PIM1gXBd11yZRQijgFN8xR +1016 EGFR G810S protein False ga4gh:VA.plbJfkC4tXllfYWs_UtsFGAkoKcGrvgv +3227 RET G810S protein False ga4gh:VA.3A5JP8pi82PeErtmpU29ppuJf4OXJh8E +3651 KDR G843D protein False ga4gh:VA.JybdlDt-1BchthSlGoC5I-K0lr2rPThD +772 HOXB13 G84E protein True ga4gh:VA.CZmfv1sEfji64jwQB3WSabehaPAPnFxJ +865 PDGFRA G853D protein True ga4gh:VA.O1HkL6H1jfFeAu4UWE5hXkfl5lxlWdcc +351 SETBP1 G870S protein True ga4gh:VA.PeKwQARIuzTLu2IfearnmVqdQ324sAnS +2008 NC_000003.11:g.10183808G>T genomic True ga4gh:VA.CSPiHR2bveiFwt1nKIJFiZwPo6WvL4jR +1858 NC_000003.11:g.10183809G>A genomic False ga4gh:VA.sw5owb4Dt3fdGn6ZMgzgs8b1G2Uvuxz0 +1920 NC_000003.11:g.10183808G>C genomic True ga4gh:VA.buQOKVsJxHRpkw_VggHxl7fEr7CDAPQI +1859 NC_000003.11:g.10183808G>A genomic True ga4gh:VA.hIQrWjD5Gc2VX_75GVyenzT0hpr1sdkT +2009 NC_000003.11:g.10183809G>T genomic True ga4gh:VA.HlMSbfwUVyOlDwu-o2UnmfraSTzvmpnt +1151 PIK3CA H1047L protein True ga4gh:VA.VkzlYLUG-zVXR5dU-rz4Y3I_twI3kUVs +107 PIK3CA H1047R protein True ga4gh:VA.RlhlEsuf37TD4nAC2ECL6onq-8AG80mw +2710 PIK3CA H1047X protein True ga4gh:VA.IXIxiKbKmAG0uT2phyTmfbcJJuNyX97Q +938 PIK3CA H1047Y protein False ga4gh:VA.Z1QMZdtOXAu2up3amTCzusY8jOkko0SQ +2957 MET H1094L protein False ga4gh:VA.5nInVFhD929mwc7NRXjlyPQ_fgo45ZKq +2463 NC_000003.11:g.10183860A>C genomic False ga4gh:VA.v8IQaKb70xoX-vx5bJwNPucDybd0g8xQ +2516 NC_000003.11:g.10183860del genomic False ga4gh:VA.u_f3m8lHsMyq1qwPfijKNWALHtDOlUzT +2520 NC_000003.11:g.10188200delC genomic False ga4gh:VA.pjVo-qK5mXrdWofOq-0r9A_gSuWTTH8- +1885 NC_000003.11:g.10188201A>C genomic True ga4gh:VA.b4giLxTTo295lMWjkgC6JYaXx1lEgnVU +1742 NC_000003.11:g.10188202C>A genomic True ga4gh:VA.edIebpBNbZxFbVmI5bKlyX2xCkC0HATO +1957 NC_000003.11:g.10188202C>G genomic True ga4gh:VA.V1Yp3Jq7dFVEqwnIQhVJZM4ukEvxSSHD +2000 NC_000003.11:g.10188201A>G genomic True ga4gh:VA.PAKXo7d7GGIh4GlB2jd9_H_JR5ZdfTKj +4112 TP53 H115Y protein True ga4gh:VA.dwCph72vfakrIkCJVE7o7PLNKlrfalXa +1921 NC_000003.11:g.10188200C>T genomic True ga4gh:VA.Ov_qWzDD_cBZQ8__lwWAYCztycPKN1w1 +2057 NC_000003.11:g.10188201del genomic True ga4gh:VA.uhq12Dn5XS4OItJBqCZYEP7wmlVwHkQ9 +3546 PTEN H123D protein False ga4gh:VA.__SK5f_2cOy-IgfmjX7MnfJwoVErlqgt +2872 MAP2K2 H123Q protein False ga4gh:VA.L0kmdbTqx5rNqmOBKrgGUdgnXtaMzSf- +2060 NC_000003.11:g.10188231A>C genomic False ga4gh:VA.g6nmeGh2WdiNdTOwIVejfSqjsQ66NiSB +3122 NC_000003.11:g.10188230C>T genomic False ga4gh:VA.iv4rLoMKphGFu7IxgV-YkVlw9SFWCn-_ +3803 SMAD4 H132Y protein False ga4gh:VA.gwbduPJ5ttbrk2xrMShuyIL7yJ5tRT70 +456 FCGR2A H167R protein True ga4gh:VA.54xz_Uz-OxsPpPkz6aBb_xKjwq4BsirG +3963 BRCA1 H1686Q protein False ga4gh:VA.ly7UOtsW4g1dg9ZSxfdDJMPif6smqeNW +3962 BRCA1 H1686R protein False ga4gh:VA.z-_UgwfgIt85GzHMBUd6BCcHmXL6RYD5 +4138 TP53 H168Q protein False ga4gh:VA.cFaI6mYPw4ZBgf8dbOaDIgkSYbkdcr5c +4137 TP53 H168R protein False ga4gh:VA.fqIN59KzDJxhC6_kk7UcdRFRFhJvyHG1 +3783 TP53 H168Y protein True ga4gh:VA.tLRfDHf_SPoZueGpyubmoF0zTvWbxUtX +4103 TP53 H178P protein True ga4gh:VA.ABv3HLwIGldUW6IvdTh5sWQFzEI_kah- +1082 TP53 H179R protein True ga4gh:VA.ykVtNd4oXy9b8ugMqsnJfZmkh45t4YLs +1083 TP53 H179Y protein True ga4gh:VA.vBl9z4GLI1ZPHsYMshmvIQ161nFbjwtT +3996 BRCA1 H1862L protein False ga4gh:VA.vz9Sw_KG6Uio7kq-GNs6VTQKbBIYrGZV +2425 NC_000003.11:g.10191578C>G genomic False ga4gh:VA.d-J8yGjzIFKj_UxWzHQghEoWMs0T9O1f +1958 NC_000003.11:g.10191578del genomic True ga4gh:VA.Kh_aKjSXUTMM0hWu8M6LAWZa9iSl8Tju +4119 TP53 H193L protein False ga4gh:VA.MwXlSaPZuDyrm-wCoBdAPZca_U0hp-xE +283 MTOR H1968Y protein True ga4gh:VA.EZ3WG0gXBfdgT7GwQR2bWk8dlOoThEcn +1595 ABL1 H201L protein False ga4gh:VA.YCqyXq2D7lKWYtgFH7usWhJopXSKxxvI +4335 TP53 H214R protein False ga4gh:VA.qvvE606Q2i0ex_4C_tS92MtOCVlQmWwW +1446 EGFR H773_V774insH protein True ga4gh:VA.6XfBRakmQhiYbVOjBfU_tQZukhaJI7ef +1513 EGFR H773_V774insNPH protein True ga4gh:VA.A0JqQsXpo32cTeDnaCSWDxaRZcj-8HXm +864 PDGFRA H845Y protein True ga4gh:VA.ObqQe_p_FKB1GSEjkRxFESgARd2Reg9K +874 ERBB2 H878Y protein True ga4gh:VA.alLLh0zbkJHqFoHN3WgAffG_f844x0ME +3529 PTEN H93D protein False ga4gh:VA.MF5f6DM2IsItf7q6p3GTHvymeHzyFEEx +3530 PTEN H93Q protein False ga4gh:VA.HwPENEmV8w4k0MiR8ou3HCiT7sg3PPia +3340 PTEN H93R protein False ga4gh:VA.9RHSoTDGE5rne7HEfrUc5FjTRwYBFe7p +3531 PTEN H93Y protein False ga4gh:VA.Om_NpZHP1QJ5QL5AJmg8Zv3gZREbsDia +4323 CBL H94Y protein False ga4gh:VA.lMtTlV-xTHzvdr8VoM7ynLiy5VVww7Mh +259 GSTP1 I105V protein True ga4gh:VA.tElRKzEHIGPv3PaTg0K8z5lddEkh-S-M +1922 NC_000003.11:g.10183857del genomic False ga4gh:VA.4GQRlBEA6gXOpNpjx2g4GYdUDsqXQ3pp +263 ABCB1 I1145I protein True ga4gh:VA.ezd6srrrVY_v1fITdT7Qm_sarom3rnKY +588 ALK I1171N protein True ga4gh:VA.Xbyg6Twqhfs57WSwN5aXHRZ2t7_GjW8D +589 ALK I1171S protein True ga4gh:VA.BUH_uWXsb1nG360k0vOQoe9qOUupYfWJ +3371 ALK I1171T protein True ga4gh:VA.t9IA1j5lXW9fUSKY5ZN1wnANLXKecZJ- +3545 PTEN I122S protein False ga4gh:VA.9jxMwrO0UBGZC4RaeCAJoD5jsHd7Tb0m +2291 NC_000003.11:g.10188297T>C genomic False ga4gh:VA.SWmgrwBXuYmSqaN-JUC0BxnxXETYfIrT +2038 NC_000003.11:g.10188296A>G genomic False ga4gh:VA.HL17JTO4zeEV-oHJls4eIG1jmqFgT-8E +2150 NC_000003.11:g.10188308A>T genomic True ga4gh:VA.l-TElvSuVA75-CbtJSj9Aar_GvtTFVxs +2030 NC_000003.11:g.10188310C>G genomic True ga4gh:VA.k1BnbFjBgO7MSp_e5jhpCUxjBtbXROUp +2476 3-10188309-T-A genomic False ga4gh:VA.EWGoi7ZWthYxHtp3MlfDryJ0Pp-h_wjr +2250 NC_000003.11:g.10188309T>G genomic False ga4gh:VA.-QSuWJ_FgFpZOp8ano5qPbWzvC9vuEXb +1871 NC_000003.11:g.10188309T>C genomic True ga4gh:VA.0oGSpdmsAmkMfIM9kkmajho07sfIZF_W +787 CHEK2 I157T protein True ga4gh:VA.dPrRsBMexSTZ_y59FF7KF0bZsxuLlB_7 +3768 TP53 I162F protein True ga4gh:VA.QlRGVPplfFi_l9Zd4Lrl9ORupJjYo7mt +3555 PTEN I168F protein False ga4gh:VA.t81RbpWfyfihrJClpodjhdhPT5O7nC7T +2246 NC_000003.11:g.10191546T>A genomic False ga4gh:VA.qVcrkqypM-WAvCtrDdkli8WHs15NKAX9 +3012 NC_000003.11:g.10191546T>C genomic False ga4gh:VA.I2s7RfQuzq7AIh8jckoeb4qMHAod9WJj +1807 NC_000003.11:g.10191545A>G genomic True ga4gh:VA.jBCkcya9Xfzz0A59NXT5znpKU0DwtaLI +2329 NC_000003.12:g.10149938delinsAA genomic False ga4gh:VA.ndCPwzek-KU626kK28bQd1gWAAk2ELze +458 FCGR2B I232T protein True ga4gh:VA.qhN7Zn8QzlWIgknzBUGC1jVoXQ5wyrSm +1598 ABL1 I242T protein False ga4gh:VA.U0VhDUd11Q5CPFHMLLPxTLS3JXbysLlx +3758 U2AF1 I24T protein False ga4gh:VA.KUja6Sh604n0-B1olnglweZ4_gtwq8AU +3630 BRCA2 I2627F protein False ga4gh:VA.MEV18vQT50yxpXouQyxVCz7G0nuGTv98 +3255 CTNNB1 I35K protein False ga4gh:VA.Rb9N_rgEOZ1Q7dQ6tiBjDWp83AsdIrhL +1235 PIK3CA I391M protein True ga4gh:VA.yfvOTi6TiDeE4EoBMAfZXmAgPzc4_9Wa +1585 SMO I408V protein False ga4gh:VA.TwqyD4GwXD3DyBy3hzeAhxSgqbgMgdQG +1615 ABL1 I418S protein False ga4gh:VA.H0C9_W0OJY0uAL8dAd8M4Uxk3CJx4EBP +1614 ABL1 I418V protein False ga4gh:VA.CFzQZ2hwzXZ3r9QkzLbWBQ1fUbaTakQ5 +2599 EGFR I462K protein False ga4gh:VA.VpJRLKfSrILO__t4EHYKHobq9BFYnhbC +2600 EGFR I462R protein False ga4gh:VA.vMthS9WsbyiByW332ggQdYHqXVxp-7W- +2608 EGFR I491K protein False ga4gh:VA.ZgJEK_D-0K615WULnjK5NjXEJPCLNTbR +2609 EGFR I491R protein False ga4gh:VA.pdO4u-YCUAUqT-OTscb6SYky9ZaPhBWJ +4022 FGFR3 I538F protein False ga4gh:VA.VDc1SDa9zQfba7tSUBAcTJYq1ss6vKJs +143 DDR2 I638F protein True ga4gh:VA.Q9puZDzAr4O5CBaiLoZbCm9EXH-egViL +2677 ERBB2 I654V protein False ga4gh:VA.Xabtm0TIhK-MK_OG5KK-_8a0YCdNXP4y +758 MLH1 I68S protein True ga4gh:VA.6NjcHEpNim-AyRuGEjR7s7vUTCqWHNG1 +2937 PRPS1 I72V protein True ga4gh:VA.1w4BM6j64LLQE4yaCgGC6sKP1B76L2er +2259 EGFR I744_K745insKIPVAI protein False ga4gh:VA.wRewr50i4vI5_pyXazE-wwTBjLg6_PM7 +3146 3-10183755-T-G genomic False ga4gh:VA.tfpxPSSvzzomNmdQDvis6yk7Y4fI2qt7 +3664 ERBB2 I767M protein False ga4gh:VA.uUvuUifkyIzkyuc1VBEU92Q5MSQEzore +3572 FLT3 I836S protein False ga4gh:VA.znUnvtNzOfTluj1696_uwKpbkaCgf1kU +3573 FLT3 I836T protein False ga4gh:VA.Nl_TstJVRlL_KToCh7zFKQU7TwGn5CfY +101 PDGFRA I843DEL protein True ga4gh:VA.e1JpPAINvv2IF9zRholJC_zWNEr12dFC +755 MSH6 I972F protein False ga4gh:VA.Oyy2WvatDfadAK98aA6HvVPAsm_IvmSD +1234 PIK3CA K111N protein True ga4gh:VA.3msOCwiDNdcuRn2ui-6Odxlzi-sNXOVQ +1120 KRAS K117N protein False ga4gh:VA.Ttcl0e7H6Kgz0i0UCr_g7-cpJhPktsn- +3584 TP53 K120E protein False ga4gh:VA.0t145t0ztXMKznWseE99nBtaOfW8ZeU7 +3596 TP53 K120R protein False ga4gh:VA.cdO-pVvg9grPJoYpo8oXA90IEQI3GnHo +3548 PTEN K125E protein False ga4gh:VA.GDhYDANBhbOAsUQDHQkDi3ndKPMobjPC +3564 PTEN K128N protein False ga4gh:VA.GuNn8scUY8aqo8efphaRd23yIYtL1uRT +3764 TP53 K139E protein True ga4gh:VA.hvHffWH3VVIQvFGM5rRPhMDMapAvV7pE +1862 NC_000003.11:g.10191482A>G genomic False ga4gh:VA.FcUK9C-Mgnwepno8PTDR0C14TFBA-VME +770 MSH2 K172* protein True ga4gh:VA.7f3hKpq0xgbTz4ml-4BuNIvO-atrzHSR +2921 PRPS1 K176N protein True ga4gh:VA.SaxsqC6iP7pKKe38pSbPD5yVtPsDs7Ai +1913 NC_000003.11:g.10191593A>T genomic True ga4gh:VA.aKOZkPNstWTWGFhLCUMjJEiJl3zTiy0C +2147 NC_000003.11:g.10191593A>G genomic False ga4gh:VA.2MQ5Artu1iHBInbojGSdMVTxRlYqIdFn +2416 H3-3A K28M protein True ga4gh:VA.ZiwLtmR_mvG_s4uHf7_GeBEbIn4ABG6N +1155 ATM K293* protein True ga4gh:VA.n0IXwABSFUk5DlAfN17a94oTXA5RII_E +3402 TP53 K305M protein False ga4gh:VA.t4u_KPLZqTLOA2bh-qBrAIwg6kLIurBQ +4147 TP53 K305N protein False ga4gh:VA.sUnAoz8dX7prVBrgQDNbBXYqHNlgoJ_4 +2871 BRCA2 K3326* protein True ga4gh:VA.wbMn_urgqh6tptIKjDMidsn3iDUGS4vz +239 NT5C2 K359Q protein True ga4gh:VA.HrL_8oYuvhvfNKpiNhAT_lX5I2Z9oxi_ +3745 CTCF K365T protein True ga4gh:VA.E9_4YwCp2O3SaKA2hgbP9_EhKvJSFTk1 +3440 KLF4 K409Q protein False ga4gh:VA.US7kggKkKTHRTyQdi1BkBpJxDBtP9uUu +2775 BRAF K439Q protein False ga4gh:VA.FeoslDpfboneBpcL8hWGqQQXD6JzC231 +2776 BRAF K439T protein False ga4gh:VA.UyI53DryOTwuNtiDwHeF1-yWefvrwPI0 +2605 EGFR K467N protein False ga4gh:VA.GSBJaGfTB3mbDfv_89kFNHCTOypStYn7 +455 EGFR K467T protein True ga4gh:VA.qaxJqw8Gmkap2tx-jyUe-4NCcyVqYDX9 +581 BRAF K483M protein True ga4gh:VA.9MTrOofqLU_m6vGUbh-FlS3pc4acH84x +2622 KIT K484_G487DEL protein True ga4gh:VA.eZUe50hjuCvY34PWm45cg2bYWEEBQmQI +2607 EGFR K489E protein False ga4gh:VA.bJanWJHfARqjpquwADQlSHvU536YPCa6 +2606 EGFR K489Q protein False ga4gh:VA.AAaQg1XBybewXD2x2x9tvYKMw9qcwKuF +949 KIT K550_K558del protein True ga4gh:VA.o8JWKKOJ1HefCBgM5r6WbOzIH02PKRV7 +948 KIT K550_W557del protein True ga4gh:VA.8wQagLQ2eG0pZq4euEZJkmFJG8m3PEcF +963 KIT K558Q protein False ga4gh:VA.4GEWxmBfjNVR82bCWxOT6swXFgQU-mZ9 +965 KIT K558R protein False ga4gh:VA.6JqpTBRNeRDGjVe6tYWEh91z7xDLdS8n +964 KIT K558_V559del protein True ga4gh:VA.w8t9IO71QG5bHkf81lvLHMfzyfhdCMA5 +1549 KIT K558delinsNP protein True ga4gh:VA.k8mvcS0Mgmgaqzjqg_1SQTHcq7R1ODOw +1272 MAP2K1 K57N protein True ga4gh:VA.sMKGT6fADsXe0yYGuvHuC85YLYoLV26P +824 MAP2K1 K57T protein False ga4gh:VA.lJg0dMlsdKQYlTWi8mpSLkVIusCSHKme +584 BRAF K601E protein True ga4gh:VA.YnV-iz1sJnZ0W7_gt2c-Bc17DxTgDlFt +733 MLH1 K618DEL protein True ga4gh:VA.m9LqTUOaChHr4fvnHHh1V52_cwRAWgvn +978 KIT K642E protein True ga4gh:VA._9KiRvPkoZgN3sRLRN28HKM0uQ1Ndq5- +2592 KIT K642R protein False ga4gh:VA.Jm5DdPAOgm8_YzheqyYUIHQxZxEhGkJQ +4024 FGFR3 K650D protein True ga4gh:VA.QHYj2X9XpgkbJI-0iFhWM59dikV4LdkQ +1400 FGFR3 K650E protein True ga4gh:VA.bKqnJPMGlvYrM7HFnjb4d48iknsnB7WH +4025 FGFR3 K650L protein True ga4gh:VA.fd0nMGNuBdQhCjUkisQ-sy4C74agnCgh +4013 FGFR3 K650M protein True ga4gh:VA.h52U7QndqLe9VuDRksrt76pFuK8Nj9Pt +3695 FGFR3 K650N protein True ga4gh:VA.30yRYol-mTE7AoQsMc6IiBM7Qq13ArLH +4019 FGFR3 K650Q protein True ga4gh:VA.6OqhOszgIhSk7-bt77DPcqmmFOqa0Hj3 +4021 FGFR3 K650T protein False ga4gh:VA.2RXebWXzp-7cKmU3WYYHO5uzF8PrVOp5 +2947 FGFR2 K660E protein False ga4gh:VA.ao-3yhKSqK4TkcNNHA1TYx4EpHk-kiQz +3166 FLT3 K663Q protein False ga4gh:VA.FMnRMOr3rTGVayWvCfBuep9v7Hdu2IVT +114 SF3B1 K666N protein True ga4gh:VA.9-Y2ZQvL5kCe0GLuveRxI9yUovIu2nyp +565 SF3B1 K700E protein True ga4gh:VA.whO8Hvl7PXuKA_tJf4Iy7VeyU-aWfFNT +3490 EGFR K708R protein False ga4gh:VA.XMJC2UPCYFWDjsSIVz0EAvwtYV2RFzTq +1638 EGFR K745_E749delKELRE protein False ga4gh:VA.4KqT6l2kce7ld1ID6xz8PNT94XwkOEeQ +264 ERCC2 K751Q protein True ga4gh:VA.gDt-MItqvvalk7B2qzRtj2HlhxQEThUZ +1312 ERBB2 K753E protein False ga4gh:VA.38-Xmn2mZACQ9tnKLrFK0BU9cpV1wJoL +4409 EGFR K754E protein True ga4gh:VA.2js3JuYSsdd-LxkTSX1eJk2C5SxyeOMO +4319 SMARCA2 K755R protein True ga4gh:VA.hNEOGlig_JTkL09Bz8tpArQR1O73wD0Z +1314 ERBB2 K755S protein False ga4gh:VA.mlxW6m1FbuJ8Gd_LhR97C746eyNADlG5 +723 EGFR K757R protein True ga4gh:VA.vrAa6gmM1XQUxwmAqJCnzwK7ghhdePsW +1895 EGFR K806E protein True ga4gh:VA.ycmXiMsinOtG-HLGcRQElwxN1trvxbIR +802 RUNX1 K83E protein True ga4gh:VA.d0l9YUy1eMmIl3IvlqT1nL2-kxOnnOMM +3666 PIK3CA K944N protein True ga4gh:VA.BsmWGmDk2hGWnSO2d9j7CjntMWOmCTbe +3669 PIK3CA K966E protein True ga4gh:VA.gfLEuCNNrMjkOBuSzlDv6XJXLUOtvVnX +1838 NC_000003.11:g.10183832_10183833delinsGG genomic True ga4gh:VA.jTJXwuBwUwinradtF3Bexi8laUZ8L5Sm +1860 NC_000003.11:g.10183833T>G genomic False ga4gh:VA.3m0BpsuoBbl0gIaVD5vMb6FAUBUsxehD +4111 TP53 L111R protein True ga4gh:VA.BOqlRAgleHphLDmpHzPLUIJhCC1XwcQR +1554 ALK L1152P protein False ga4gh:VA.Gkr5posPzyNh3jGXMBSvEa2RA968Spbb +307 ALK L1152R protein True ga4gh:VA.Jq35Z7RgLnGxUZaDZZbJR_AkvW4c-yq0 +4332 ALK L1152V protein False ga4gh:VA.OZqEMWucAqmx3U3oo6wz-tPEeZDM-qjh +1820 NC_000003.11:g.10188203C>G genomic True ga4gh:VA._NtNh9241v2h9aTp7634LTXmo17hmcqV +1798 NC_000003.11:g.10188210T>C genomic True ga4gh:VA.d8CWNTb2fJ-o0sUgpAT6pzEDwwVIULoE +1822 NC_000003.11:g.10188210T>G genomic False ga4gh:VA.7rXEL0K6tdffVyc23Ex5NcCBfol8jLRp +1841 NC_000003.11:g.10188209_10188210insA genomic True ga4gh:VA.IurXi9shPHhWOrxjoJR3t3DrJoTQFtjQ +4324 ALK L1196M protein True ga4gh:VA.rdhnlJk8MzBxdYL4tHC4gHvUyciQw6KW +1553 ALK L1196Q protein False ga4gh:VA.mayrIxRXCmkNUFQCTcKEbanE9NbSKOIW +1275 ALK L1198F protein True ga4gh:VA.z6WahzspU2ffx6LlHHNzTHHcyjbZJcka +1556 ALK L1198P protein False ga4gh:VA.LNGwAaGtHYyaCX2gMoOkZKvts17OXsWF +3031 BCL2 L119V protein False ga4gh:VA.RTJT-2dsec5jg-8SH6D_ob2HlmQlk38t +3032 MYOD1 L122R protein True ga4gh:VA.PjI6q2whVbPLztHp3ArIpq71E0cUS5lW +2168 RAD50 L1237F protein True ga4gh:VA.hne9Bf8llWb709HTrz-OCORKOLz3Secs +1851 NC_000003.11:g.10188238_10188239delinsTT genomic False ga4gh:VA.TA6NGvY0ynGGN0X1Doq2Wma41_sKCEqy +3066 3-10188239-C-T genomic True ga4gh:VA.8qmagPADh0UyKOHAxHMEkd3HsoVTUXix +2157 NC_000003.11:g.10188240T>C genomic False ga4gh:VA.kfPMYhCbUC__tQXB_Bm1l3A3L8ka2vzX +1886 NC_000003.11:g.10188240T>G genomic True ga4gh:VA.6prQYtd44kD6D8dIuzyPMTNwURoSzCNa +3068 NC_000003.11:g.10188238del genomic False ga4gh:VA.7jIdgftE5dt7X_CJ1pBScZ58SOExiKH9 +2508 NC_000003.11:g.10188243T>C genomic True ga4gh:VA.LpLmEeHdkdsndxf4wn7_7tVDQ497eywD +3660 CYSLTR2 L129Q protein False ga4gh:VA.nkBk1Qj_otg8T9PZuwGxRY35F2j7le9h +1099 TP53 L130V protein False ga4gh:VA.Hi9_MYGPH-IoYmOf3tc8DhTuEaF8l3Jl +3078 VHL L135* protein False ga4gh:VA.hwa_m54wRTPvq25vUXbFI9mO6hs-IJTD +1769 NC_000003.11:g.10188261T>A genomic True ga4gh:VA.Cih1ycHkkMDhJ82WMEBHwtz0V7BDmRzw +1906 NC_000003.11:g.10188261del genomic True ga4gh:VA.ibAsNQ-bNaLMSdQMYM3yTmE88BlQidec +4273 BRCA1 L1407P protein False ga4gh:VA.4KmM_6VsbuYF54Z8UMVQJh3HsndeeLay +2559 NC_000003.11:g.10188276delT genomic False ga4gh:VA.S2Juq_qHaMmwGW2jbG9FEPxW8A4yGwZA +1923 NC_000003.11:g.10188315T>C genomic True ga4gh:VA.1eRS8lHHoF6RUOOtcYOuHtmgaWTAbdac +1032 NOTCH1 L1574P protein False ga4gh:VA.KkrqUva4XjskUnr0LILhyjz6Wse6sTFy +1145 NOTCH1 L1574Q protein False ga4gh:VA.DcnFuVY6B4hVTmq8Wgz8M2IRE0Jw5Jey +1142 NOTCH1 L1585R protein False ga4gh:VA.kMfxl7-Rg2izbCSVuAk80QBSROIV7inO +1738 NC_000003.11:g.10191480T>C genomic True ga4gh:VA.g3SXC8c83bFEX6JLoEnCo5P2C-49VerF +2467 NC_000003.11:g.10191480T>A genomic False ga4gh:VA.fCI38_aMeuYasmJFQXRFey-mGY60ZPQ4 +1803 NC_000003.11:g.10191479C>G genomic True ga4gh:VA.Kw_tBIilmUHmX1O5sEBh5irlTiHNxlu0 +4449 ERBB2 L15F protein False ga4gh:VA.-6mbnrf3HG29zkCgyxSqcCUtshbwe4bq +1031 NOTCH1 L1600P protein False ga4gh:VA.nqRSGh2pwDSnZDi5ry1-gzKVNRXjQKaE +1140 NOTCH1 L1600Q protein False ga4gh:VA.i4PMKJws1Eg0lwaUe62UuQDltezLGuEg +2505 NC_000003.11:g.10191494C>T genomic False ga4gh:VA.i1_mk2JGybbUMUlgxSlZKy6hUzn0Jz36 +2033 NC_000003.11:g.10191495T>A genomic True ga4gh:VA._fGoTVOpJNTU5Wi54qvhfhnfbGoheMwW +3198 NC_000003.11:g.10191494C>A genomic False ga4gh:VA.fsKHgfumx_WcSwMx3RdBavc6g90BAFSS +2478 NC_000003.11:g.10191495T>C genomic False ga4gh:VA.xMqUSQrxTKnfD5g1zQUi2Hq8riMxNs98 +2563 NC_000003.11:g.10191495delT genomic False ga4gh:VA.jUeT1n4AuBzwtt5TT-Iaac1KasATWjKE +1034 NOTCH1 L1678P protein False ga4gh:VA.NTdE97B5tT_QV9rc9ujARKDv7AXdtcq2 +3097 NC_000003.11:g.10191512C>T genomic False ga4gh:VA.4A5wjiY4LFCWMhX9oCyG3xTgaQrF-KcB +1887 NC_000003.11:g.10191513T>C genomic True ga4gh:VA.9HDDV6D5U96bW2CzejmnP7yDuRaMxYJh +2326 NC_000003.12:g.10149828_10149833del genomic False ga4gh:VA.44jlW9FLYpwWke-78qtueB4pUoWnZaq6 +3335 CDKN2A L16P protein False ga4gh:VA.jFfbj6Ga6vaywcoV-lFXtdsoUjPJpEKE +2675 MSH2 L173P protein False ga4gh:VA.EYRVNESHFhI8QKLZw7AzGQO1-YFOo9XE +3982 BRCA1 L1764P protein False ga4gh:VA.XsC2nozh_m0sJVLGoHxw-17lwBPdjSfS +1748 NC_000003.11:g.10191540T>C genomic True ga4gh:VA.FsXb6mqvmU6dtkQZikPLpnlKv9isU5tI +1997 NC_000003.11:g.10191540T>A genomic True ga4gh:VA.rcjIhLw_1WPHeMKR_YFGi8dBuHs6oCxP +1888 NC_000003.11:g.10191540T>G genomic True ga4gh:VA.ADbgp1-Gfe5eAUkm_N2DF5CEbk4dO5_n +2070 NC_000003.11:g.10191558T>A genomic False ga4gh:VA.WuKkWOCbZIs7hpYtBqkEVtmFxB_zdZ18 +1776 NC_000003.11:g.10191558T>C genomic True ga4gh:VA.zyN_Z_szGeKDA1naEocc7lKsVwgHeWEF +1808 NC_000003.11:g.10191558T>G genomic True ga4gh:VA.W-HNr44hfwVMgVP65ELR9lQG9mhZyMGM +1852 NC_000003.11:g.10191570T>C genomic True ga4gh:VA.ruRrfY75EzGba-4hUu03ocYDuguscLzm +1861 NC_000003.11:g.10191570T>A genomic True ga4gh:VA.c-8lxy9XQVr11djpNxFKqXEFlO6Q9eCu +1924 NC_000003.11:g.10191570T>G genomic True ga4gh:VA.us_1Nbp9jvxxlkhKFVv8eqxz5M6ANq51 +1836 NC_000003.11:g.10191569C>G genomic True ga4gh:VA.R-d42p33UwGGonl2QnbDjJ-0WGo4VCc6 +2139 NC_000003.11:g.10191569del genomic True ga4gh:VA.NWlzF4aQ21-L40z4WvwdZwBJSg9wpyQX +1828 NC_000003.11:g.10191570del genomic False ga4gh:VA.b_aGFGbbSnjG1kd8jcvMHBAuFcMnJ9TK +2919 PRPS1 L191F protein True ga4gh:VA.YK2ROyJUUoyaoUjJv7HjsrbArPHrG4I2 +1078 TP53 L194P protein False ga4gh:VA.pPfIS3brSRbZ3sBVAjl-fEavwjhvcTHq +3392 TP53 L194R protein False ga4gh:VA.xoaDX04b42Jdz2zaUP5JB4RWUn5U8SLd +2501 NC_000003.11:g.10191600T>C genomic False ga4gh:VA.C24d8HgNOKLegPLs91M0xn7cI0xAqofy +2010 NC_000003.11:g.10191600T>A genomic True ga4gh:VA.fcw31joX5ID-14njJoSSTkbCaChu1JN0 +2247 NC_000003.11:g.10191600T>G genomic False ga4gh:VA.YH6OdKUWN5g0dUQ7ql9L9N0hPtgTMQa9 +2543 NC_000003.11:g.10191599del genomic False ga4gh:VA.XRSjda0o1CmL5ASG98rhDGp7j0zRCxMY +2716 MTOR L2230V protein False ga4gh:VA.R7lqEi62MQYRZB8vYjerrSFBNE3vFzRk +140 DDR2 L239R protein True ga4gh:VA.NleGwR89czfHsIuu0CdIbZ6y0efrdFWt +1163 ATM L2427P protein True ga4gh:VA.47RXO582IblItpEuZPIVMQ9B0YKaKNMQ +3414 MTOR L2427Q protein False ga4gh:VA.ApDtZFEwpkLjAFyzjEMfs2JD-42SaAQZ +3755 BACH2 L24P protein False ga4gh:VA.-IJ0PvaU6aPsl6iRHShEbjHddXV8FFVg +3624 BRCA2 L2510P protein False ga4gh:VA.AQH3opjg4avcfZ2KztNuEFe64yM2XJVd +3771 TP53 L252F protein True ga4gh:VA.iYWGXsYkaTDc8UhNmBqw9iTJ7YqX6I_w +3801 TP53 L257P protein True ga4gh:VA.m6BXxZBreN6NEk8g0RD-OxFHLJ4Vbm15 +3640 BRCA2 L2647P protein False ga4gh:VA._JV2pkMYA7FqDsuYek0fx8hdRykeLMmb +3642 BRCA2 L2653P protein False ga4gh:VA.zbTDmqQDGdY2WNU7eFeN-IQ2Ap6TOoFD +3612 BRCA2 L2654P protein False ga4gh:VA.vANeRLnO3AQ1WKWKUygf1eJDSsyzK33D +3638 BRCA2 L2688P protein False ga4gh:VA.6sZI_VVIXB_ZoaKy5Y_Uko0fFt7o2nuD +1602 ABL1 L273M protein False ga4gh:VA.u0MdLgOkwdqKP8OEpH3ER2NjVBefE6cV +3617 BRCA2 L2792P protein False ga4gh:VA.j264NPGp9ImrnZOjwACHLZXxyZLprAY6 +1506 ABL1 L298V protein True ga4gh:VA.qyz4EGd2BhO7k7JiruW_1GtQ8-05VA8e +3643 PIM1 L2V protein True ga4gh:VA.SGXQnyI67stJcCYkUdTPo_6Zz3MEFX0m +4125 TP53 L305M protein False ga4gh:VA.Y3dTuD7d26kmqEy9HjaaHZWz4Qr6wHEb +3775 TP53 L308M protein True ga4gh:VA.NP0ze0vzWcR_Qev6oObA_-vK7lWWZt-J +4322 NFE2L2 L30F protein False ga4gh:VA.RSC3O6ncUkPC4G6gSWtmdjv5QwAZNi_4 +3776 TP53 L323P protein True ga4gh:VA.xgqstF54p1VPCPQoJtoqk2ADuvwWwxs4 +3580 TP53 L330P protein True ga4gh:VA.YTz0nPUx9gmzDKEKTaiKBhmILRBCa-4m +3581 TP53 L330R protein True ga4gh:VA.kYVXMi9t5Qer9CmXJ_8UYhSylR8rFkKv +3583 TP53 L344P protein True ga4gh:VA.jsyWeq1bQebfSY-AR5eV9P_W1o-JuM7w +1570 SMO L412F protein True ga4gh:VA.JZXwoXlvsmlSiQDYGYIYtJfnp_IARHC_ +4313 POLE L424I protein False ga4gh:VA.VjfcFE7DDysP0wQamVuoYXjr5XXUEZgF +4158 POLE L424V protein False ga4gh:VA.lN1M09gvpGPkL4elvta2DbATRC2akF8y +2842 MAP2K2 L46F protein False ga4gh:VA.Lmhgm1hyEgFHUa8ox7CSBZUd9nW5NFxS +2804 BRAF L485F protein False ga4gh:VA.CQzCmAk2IlmmA3zzv1_WDF83iPGifQbs +658 BRAF L505H protein True ga4gh:VA.D-AE92d-4-GzUMxCnrjN9Qpmsg3Ju66k +2793 BRAF L525R protein False ga4gh:VA.7xW7txZMVAzkQd3hG6fFocTK6pGo-ULi +1191 AKT1 L52R protein False ga4gh:VA.l3bp9cZv4WO2uchZeBG5qh72GZsZ05fV +46 ESR1 L536Q protein True ga4gh:VA.Bbh5uLL_7mZ5X6SHg58E4htO_cKQrKHn +1675 ESR1 L536R protein False ga4gh:VA.IHaGpVa2G7qyZqJ-8nRGiFgL-SpLW7dK +72 KIT L576P protein True ga4gh:VA.z2MmOn-EKde3j5N0335DbKXvMRHZ8sfg +3705 AR L57Q protein False ga4gh:VA.XwyOCtl-aYVlvLwofWOvikqqxiXmJ9ne +3451 BRAF L596V protein False ga4gh:VA.Xvo1nbADOSgbOlFTNX3H-vOQeWaresdo +583 BRAF L597Q protein True ga4gh:VA.qHeIdV-N3Jvs_FL3SBoitkd64uurRKzq +288 BRAF L597R protein True ga4gh:VA.Uny06oXdQbnS-ctgJaY5WYaO277MtWaL +582 BRAF L597S protein True ga4gh:VA.St5RlZnuNPPGcpcsZxlSyYybsOqo8KyO +585 BRAF L597V protein True ga4gh:VA.R5tGJ_JvhEkc35uWVOP24Etqe5zz-LWT +2401 FGFR3 L608V protein False ga4gh:VA.mLJuut6EGQfmnqbDologo0OieILsrX7w +1944 NC_000003.11:g.10183719T>C genomic False ga4gh:VA.MtVLXfh32idW3E3Hf3R1veZVTQYi39CL +139 DDR2 L63V protein True ga4gh:VA.VyaKKO-WbQNY6ZdehwUpkksx5gjtds0_ +2999 EGFR L718Q protein False ga4gh:VA.65A4A78Nm94cbDU0x8prdTawpKmpsZXv +3000 EGFR L718V protein False ga4gh:VA.Ku_iaU6f1Wa8GeWh5Tlz1X1NPBq414Bx +1891 EGFR L747P protein True ga4gh:VA.F5-t68SOA30ViFZJcmBCRhDW33N4bO32 +1006 EGFR L747_A750delinsP protein False ga4gh:VA.nTXkTPxvOJn7DmRmMg-jxOLONzzUkBHe +1012 EGFR L747_P753delinsS protein True ga4gh:VA.n5zAXCUPQX16GseagfDuXnXvGRlwiuyD +890 EGFR L747_S752del protein False ga4gh:VA.p0AQ0gLxcBszQG5ZR_UYwZD8wCssLDx0 +1580 EGFR L747_S752delinsQ protein True ga4gh:VA.1N9WlPYnTAObq0SX1BtH8533F4o6w4qy +1007 EGFR L747_T751delLREAT protein False ga4gh:VA.bm2LEMqrbwCupLdsz9p7_ah6vf_M3iAZ +1010 EGFR L747_T751delinsP protein False ga4gh:VA.eDMXxJw9shlSKF3znIg5abniGoyJ3GQ4 +1008 EGFR L747_T751delinsQ protein False ga4gh:VA.nTmRFyjPrx0IJSZN6kNVmI59dU4Y3EAm +1313 ERBB2 L753E protein False ga4gh:VA.fb1zUr-f82hMRgMjEM1wQ_6_fPCJ9-Sn +1304 ERBB2 L755P protein False ga4gh:VA._zGg2DBna8lXy-XhoYpOWqpWrrBJl5AB +39 ERBB2 L755S protein True ga4gh:VA.2H6jC4r6bxSvihY72MAGuTrAPedjjCnE +40 ERBB2 L755W protein True ga4gh:VA.OovHsd0b4tUhwGzHxCI6bt5P6bg4yK8w +37 ERBB2 L755_T759del protein True ga4gh:VA.rFwsfnekdWjwKNmsAw9fZOCGgIvcMnCn +1308 ERBB2 L768S protein False ga4gh:VA.HpmvZN0lYMMasO1F5HIkIIAJ1lkZXFxl +4477 BAX L76R protein False ga4gh:VA.E09DEPTq-wGeL1U8XIu7qeKQUjYADtVX +3004 EGFR L792H protein False ga4gh:VA.iPZUgQGTZNhRbkdKff0o1PlhAzv02ENl +1457 EGFR L838P protein True ga4gh:VA.y8P5CTs5QXLhN-VIRZMGaKk1SOTq2Jir +1018 EGFR L838V protein True ga4gh:VA.JwyElRnPWcDRLOkRjICvCIyqdKNJOwXv +3648 KDR L840F protein False ga4gh:VA.loGtaGwmnIUzrbWkGDzOyhGDVEGB1gic +1473 EGFR L858Q protein False ga4gh:VA.MpQOkHHsIwzY5tZvC29XPoCCs-dn1u2Z +33 EGFR L858R protein True ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA +2020 NC_000003.11:g.10183785T>C genomic True ga4gh:VA.sjfbnDp1QRIDFQs-XDP1TnDIjik1ySmM +1020 EGFR L861Q protein True ga4gh:VA.i8en13LmRotcbzd1VXlprrXmZYY_n8Ht +1477 EGFR L861R protein True ga4gh:VA.BGL6zgs5v1R7OGC39hqygTmAjSuVgbBP +496 ERBB2 L866M protein True ga4gh:VA.A0e8aHaxrj7VVhS0i9Gi6KY3JeUW4N_u +2330 ERBB2 L869R protein False ga4gh:VA.DaUcw05tyAFsUsBpHl7X8EHb0xMEYd2p +2308 NC_000003.11:g.10183797T>A genomic False ga4gh:VA.ETjAWSsWQI3BzDWIsZ20Av3enrDxbzBY +1793 NC_000003.11:g.10183797T>C genomic True ga4gh:VA.OZBgdHmvzMVVqsBDlN6xEzInCcYE-Wqh +2549 3-10183797-T-G genomic False ga4gh:VA.fz7SQZLqk0ck66TAF_3Z0Unyuyoz1tOY +3670 PIK3CA L938* protein True ga4gh:VA.opUWp0rCcP9ZOZQaR2E6iVEpInPqiaS2 +937 PIK3CA M1043I protein False ga4gh:VA.TdExGXHZflky6uB4RxkWLqDeUWSTeH59 +2940 PRPS1 M115T protein True ga4gh:VA.47A9bdGWBJozeqkAB_fzG5QqOzLKCySX +3301 SPOP M117I protein False ga4gh:VA.fzFI2vg9SMXZbR2e9xeSa8X9iaMKG8SL +3280 SPOP M117V protein False ga4gh:VA.DRLyLXtrZfIXLX2j4Qy2n_NLyYx4xY7t +3372 MET M1250T protein False ga4gh:VA.Z8QOVKukWH2QcenbPEMs7n1RQZ7xR_x1 +3966 BRCA1 M1628T protein False ga4gh:VA.XT6wfjWDDUmcKfr0fcOidEnbcBlHuQVJ +3965 BRCA1 M1652I protein False ga4gh:VA.bf76ZCy_g69UHN5OUR7zbT1mrU8oVGTZ +4401 BRCA1 M1775K protein False ga4gh:VA.lq1XQdWDLlIcTJcUqOrjI2QdDGDja2hQ +4400 BRCA1 M1775R protein False ga4gh:VA.OCfyCKMUR3IpIxnKBQSUA2svnaWB3TT8 +847 NC_000003.11:g.10183531_10183551del genomic True ga4gh:VA.Y8zuj7Rdfu-7e546mLns1g6uU8G9SoNL +848 NC_000003.11:g.10183534G>A genomic True ga4gh:VA.NIPSPlZwoa1pg6zd07et4tTfQoKVz72n +846 NC_000003.11:g.10183532_10183548del genomic True ga4gh:VA.IZJDmP_TAxVOH5W3HGqrGsBf_HwUB8us +1248 BRCA2 M1I protein True ga4gh:VA.yl2HtUlSXdzcf1GQ9Ic090fhNsnIRnGS +747 MLH1 M1L protein True ga4gh:VA.lZfJCuXrqZxn_M2xm6hz755QBSHTRm4O +2868 NC_000003.11:g.10191638A>C genomic False ga4gh:VA.4y9RYpnZfg8-jC2R91a-fWBDMswOI-i7 +609 MTOR M2327I protein True ga4gh:VA.a_RubaFaGvGxhMdYnbpRfNxDye_z8PhS +1066 TP53 M237I protein True ga4gh:VA.zc1EBGpEL2ul7A4qGTZeKUGhmZCM-4z5 +1597 ABL1 M237V protein False ga4gh:VA.WBVzW9mCNVxECh9AF7OSFFcyacIc23iN +3396 TP53 M243T protein False ga4gh:VA.5xSvXvqd5qUop1zO01GAtjlvugzx0scj +3398 TP53 M246A protein False ga4gh:VA.qZOhvpEWDsTHfk09oJ8GfBiwvl44TqyT +3789 TP53 M246L protein True ga4gh:VA.hntaSbEBlmjRsqTlp1jCiBA8c7Hu5_OO +4105 TP53 M246R protein False ga4gh:VA.5a5Lp6U3iCAnncRYl_yoIR1TqL08D3_I +3399 TP53 M246T protein False ga4gh:VA.iogAaToiqouUws8H56sIPFxf1on4bZUE +1610 ABL1 M388L protein False ga4gh:VA.hrmKsagllbykJPwPARF45SikzD0GKXpA +1622 ABL1 M472I protein False ga4gh:VA.P31bC60-m53FnVsBBY4OdziE4D4ebSxB +769 MLH1 M490T protein True ga4gh:VA.RfIHU8NAM0z2fiPvh46AyPIeRHuyJDig +1288 JAK3 M511I protein False ga4gh:VA.qd7dq7ybsIeDC4f6GJo3bZxOruexl4li +3515 FGFR3 M528I protein False ga4gh:VA.WMeKIx-DDzu_HbDo0ejE3QKJ3gO3Yk6h +201 KIT M541L protein True ga4gh:VA.Xk647UAYt8ZXmpkgLgC9_Y1r--18ZUBa +2177 NC_000003.11:g.10183693G>C genomic False ga4gh:VA.steH614pjaf0H4aruvSR3eew5A3rXbai +829 NC_000003.11:g.10183693_10183697del genomic True ga4gh:VA.I7j3_ZdAc0b00PH7q7YudhQQ4n4c9cr8 +951 KIT M552_W557DEL protein False ga4gh:VA.-zfP9i2F0ZvoFvMQno8aEX7Ih6JFfFqH +3165 FLT3 M664I protein False ga4gh:VA.xm5AG1VIEtFCIGbGAYyWSUSEbPUx5g3j +2745 EGFR M766Q protein False ga4gh:VA.gNOrTf9EgIrRxIQlG6JOiCeCvNdkQjUA +1664 EGFR M766_A767insAI protein True ga4gh:VA.tWS7Xm6G5NBIpMLpG6sYirQQEEuRXge_ +2213 EGFR M766_A767insASV protein True ga4gh:VA.sHKHDIuSUmV08aL2O-J3T9KpVc2-9SXN +818 ERBB2 M774DELINSWLV protein True ga4gh:VA.rcLKoiGNySE40iXrrsf9S0PrT5NIIq__ +3588 RIT1 M90I protein False ga4gh:VA.VU5wtffe7WT0XxDxtuKAgxpPFK-X0PoI +113 RET M918T protein True ga4gh:VA.GweduWrfxV58YnSvUBfHPGOA-KCH_iIl +3438 PIK3CA N1044K protein False ga4gh:VA.AFHkUoNUqb-IMH-_1b0E4V1Z1oEY6_Kr +2924 PRPS1 N114D protein False ga4gh:VA.UcZzVhHaF4vw1g1rSMBzxyFOEdNvsRYi +2843 MAP2K2 N126D protein False ga4gh:VA.E6vrqxjyN3Eq43J82ELzexuo_t3ECXya +778 SLCO1B1 N130D protein True ga4gh:VA.FUd0fYmp-yAbQolcHg1jZyAXcgyulm9s +1953 NC_000003.11:g.10188250C>A genomic True ga4gh:VA.OKhTB99uP4y93wBt2fJQbtNAcRMpP6eY +2460 NC_000003.11:g.10188250C>G genomic False ga4gh:VA.o7mO0AwoHoSl705UkWDWosY7FOA0Kwlb +2001 NC_000003.11:g.10188249A>G genomic True ga4gh:VA.Bxr9v7VOkmkxfpujih03miW16u1OLIKO +2580 NC_000003.11:g.10188249A>C genomic True ga4gh:VA.HV7BOXJn1qOtmrcdnoB_5uMRBwmJY3P2 +1800 NC_000003.11:g.10188247_10188248del genomic True ga4gh:VA.sdjAIH04BvIrEuVBHxkxq8UoWsNggATN +1868 NC_000003.11:g.10188250_10188251delinsA genomic False ga4gh:VA.DCs1gpLZHnbx4J1X9WPXyl9LoAouQJvO +2317 NC_000003.11:g.10188277delC genomic False ga4gh:VA.gd_d_VBwEiORgSrBehPfRRPUi6lIax55 +2318 NC_000003.12:g.10146595_10146601del genomic False ga4gh:VA.5YleJx-mK0lsDv_3BZoDstB3OpPgCgT3 +1917 NC_000003.11:g.10188279_10188297del genomic False ga4gh:VA.CSWNhR5w_geMmJTxkbO3UCLCvT0S2Ypx +2923 PRPS1 N144S protein True ga4gh:VA.gveIT6ggjvrfA8D1FiKRQ-dg65R5_zM8 +2162 NC_000003.11:g.10188306A>G genomic True ga4gh:VA.6Y_QeoafunCefEToZz0BBp5NpHD5fZAM +2561 NC_000003.12:g.10146620del genomic True ga4gh:VA.9VFNSKIDMVytqKZzeijQh6WAxsnEEuYj +1770 NC_000003.12:g.10146622del genomic True ga4gh:VA.7b7n_45c6JB1o-g7xsECmpvvRIWoFlB0 +3281 ERCC2 N238S protein False ga4gh:VA.F2FwB5cmIflFU2R0AsW6XD0MLLpE3zO_ +3394 TP53 N239D protein False ga4gh:VA.h2h9lGcfvlIjoB3RgHvljim85E16LiMT +3787 TP53 N239S protein True ga4gh:VA.yELVq7C1ePNZ_VFSDhX5t0td_iy_P4xP +3395 TP53 N239T protein False ga4gh:VA.L3rUq3KPFWwWadFXI5GI1ysJnj0D2Ffv +244 ATM N2875H protein True ga4gh:VA.3WYMoLv5oswoGz1WVrgsp7iOf2KhXEaK +3641 BRCA2 N3124I protein False ga4gh:VA.B3jDogRJ5ZbKxUQZvMaChKTKuIzocR_1 +930 PIK3CA N345K protein True ga4gh:VA.5ZAVMcpcV5Et3PyR9fDGR9fK3GRMYXTF +3679 ETV6 N385_R418del protein False ga4gh:VA.s031Mklr50vns52Nx6PN3gbWBhG-7ETn +3681 JAK1 N451S protein False ga4gh:VA.B9ZkvyWm7-wBwjGrInk54GQvvsukQhqf +2794 BRAF N486_P490del protein True ga4gh:VA.1moxgQ3AxfqimQilhDn94nHU24vmOpU8 +3237 KIT N505I protein False ga4gh:VA.iaWTHnjcD5nzAZ3ofHdKnvTxdyZ-aesJ +3238 KIT N505R protein False ga4gh:VA.4Z8xxVAQ3snYLEJizaVVMiva3-HWPJqG +3216 FGFR4 N535K protein False ga4gh:VA.TGfVLAhS8POn-kpbRmwxoPpJj4ONijWz +4028 FGFR3 N540D protein False ga4gh:VA.Vfg2OOcmmZkz8ijLSEcsWkH9695GEm1n +3693 FGFR3 N540K protein False ga4gh:VA.zZ4xq287mqYySalGnW2JL-A7ZaemIcLU +3694 FGFR3 N540S protein False ga4gh:VA.bJpJV9vSppRvKw6DiOM5lyd2yFxpghEV +515 FGFR1 N546K protein True ga4gh:VA.1NUXEJurUWhzTxg-ECap49qQtS7WS7ds +2780 FGFR2 N549H protein False ga4gh:VA.fsmabl-s5rjCUHg0OAjcW3FmI0aVxESY +545 FGFR2 N550K protein True ga4gh:VA.pMg4lMILoFfK4S51pu6jKNsbA95vPdH1 +751 MLH1 N551T protein True ga4gh:VA.FAZ9HS9O-z-KtIAGUQj0xghohk3X3ITj +1652 PIK3R2 N561D protein True ga4gh:VA.-rjiZ2l3leWMFBN2eOTc3mGggbONc-yc +4014 PLCG2 N571S protein False ga4gh:VA.Uuag5Juaxfn7WrJgfZlVick2wju0BIyi +3444 BRAF N580S protein False ga4gh:VA.GHIe4Z0CKPNdz6v2irW2XjCzAdUctp4P +1186 BRAF N581S protein True ga4gh:VA.MyTD-oUKGXdQ7K5Ouq94idPSPEmoigkK +3053 FLT3 N676K protein False ga4gh:VA.sJlMgNlx_syJ1afz3xoJDifs5x_Xp1p6 +3304 EGFR N771_P772insL protein True ga4gh:VA.kAZ8gzHVDZZWYtsxiIFouAnVbxuIW4DD +1662 EGFR N771delinsVH protein False ga4gh:VA.-jNMoaVSsArAQ1vReD13bIvQAmHPja7i +2112 NC_000003.11:g.10183763A>G genomic False ga4gh:VA.5Qfc2Ixq9-7Gg-V0PB5mW4BGUzmCOU1e +1754 NC_000003.11:g.10183763A>C genomic True ga4gh:VA.dTejxD7z1CSu6SeWiIitoAANka_qva30 +2037 NC_000003.11:g.10183764A>T genomic True ga4gh:VA.WLnP00p7ujtalUv-pCtucHkIkYkPhxmp +1755 NC_000003.11:g.10183764A>G genomic True ga4gh:VA.BybWSsbmn_2YEhFvoNRPhIBl08kqCbIw +1756 NC_000003.11:g.10183764A>C genomic True ga4gh:VA.eZOXgglXU3aHJZvp04eZoobIASs0xYFc +2113 NC_000003.11:g.10183763A>T genomic False ga4gh:VA.BsAPaAegHriKyN-h3cyLhSSBB-Y4zHlM +849 NC_000003.11:g.10183550A>G genomic True ga4gh:VA.0yUQbEdPtddrU_WFlDhmvqC-Aje-N4kr +987 KIT N822H protein True ga4gh:VA.jaB0I0_cwSEr-YXaDTYMQb3EwRZDxH93 +1263 KIT N822K protein True ga4gh:VA.RdNS9ziiegw-IQb56PMRjRn3wRVV1Rwj +1188 EGFR N826S protein True ga4gh:VA.uN4s-fvPtpRs8_C-58I4poepFhY7l2Dv +1896 EGFR N826Y protein True ga4gh:VA.83QdlKy_qLChCJkklKdnoSMzKn186Bvh +3201 FLT3 N841I protein False ga4gh:VA.rXHqFckVAIX2SpbhwvpIHQiJTPY2vZDK +3213 FLT3 N841K protein False ga4gh:VA.3Xg4luzxMeUWH8YFtDWAg45Ce69T3N_9 +3308 FLT3 N841T protein False ga4gh:VA.9nCkqtqNeFwav2Ilhpo-Ty524MUvs1rh +1899 EGFR N842S protein True ga4gh:VA.iVhfLhfuGsLw6hR8J24iwjaBKl0QRn5s +873 ERBB2 N857S protein True ga4gh:VA.709-h92tboZGaNRTwwSjtpt9jj33KZlR +2878 NC_000003.11:g.10183799A>C genomic False ga4gh:VA.i5PEsFVQyXLwywRkBnLITyEVtxP2pFTl +2149 NC_000003.11:g.10183800A>T genomic False ga4gh:VA.ezFS8xauJ-sp9YbU9MuN7ACiwLKnNDE1 +3532 PTEN N94I protein False ga4gh:VA.q6Lbd19K9bs38WooJ1Bgq1sHypF4eoGe +2058 NC_000003.11:g.10183836del genomic True ga4gh:VA.lGMKn6yl5jJK8etyfnrj2V-YOSFXqjD7 +1927 NC_000003.11:g.10183838C>G genomic False ga4gh:VA.hnZ28qiBlP8E7tF_qLr-WkkRXtsqdqie +1795 NC_000003.11:g.10183840_10183841del genomic True ga4gh:VA.JZM1vpvVD7BXifZ_JUahanmHW_G1d2Sf +2118 NC_000003.11:g.10183839C>T genomic False ga4gh:VA.cyfnIcLis2kHVa9lOxVZ9t4SwmDKECfy +2837 MAP2K1 P124L protein False ga4gh:VA.Uhggl0kfMZ_MaFNo57-aSkvjs3BtjdGj +82 MAP2K1 P124S protein True ga4gh:VA.NpMjHiloC60aBs7qR5S_ms1CZIwzeUhc +2866 3-10188271-A-G genomic False ga4gh:VA.coOoxepuUAaPpv0tiIb3lTzWXFXW0RU0 +2120 NC_000003.11:g.10188270C>T genomic False ga4gh:VA.OLO-neEQR3b3dfV-UY5Y5yCjx1__U_yT +2440 NC_000003.11:g.10188270C>G genomic True ga4gh:VA.XDEiovPy0OUCecNv3gaKeIR9R-fpk_Os +734 MLH1 P138T protein True ga4gh:VA.rtbFD9-5F9M2j35NMenHtdLLqZ0XnMRP +761 MSH6 P138T protein True ga4gh:VA.no0DvftgxBmpCLi8sFJz_QaJk-Jz0ae4 +1928 NC_000003.11:g.10188269C>A genomic True ga4gh:VA.-Vc2fGlhLrMrDAGYMc60wGhDwuJwhret +1644 PXDNL P1460T protein False ga4gh:VA.L-G9rIJKOwJ2yN22Nq5KzEEyDDaMOKmS +2055 NC_000003.12:g.10146610del genomic True ga4gh:VA.DN2daxbNTuvdFjz0ZqbvF3gy2LQTCYKL +3418 TP53 P151A protein False ga4gh:VA.OD_xbuYA9Ayo2BpTUKpLDwZOnLUXVkhk +1093 TP53 P151H protein True ga4gh:VA.QcrB2xOcYOIHq0M220ZKZAfPz9GPVAlA +3765 TP53 P151S protein True ga4gh:VA.Wv54HQ7rxdyOu7viwwj1dfDQ2vHSzW52 +3767 TP53 P152L protein True ga4gh:VA.VPDpGOPBtgWZ1VS-Di2iUP9gvRYokk5S +3794 TP53 P152T protein True ga4gh:VA.5m7Wn3hol6iqESRcD-JH6GaNqJCnrYm4 +1962 NC_000003.11:g.10188319A>C genomic True ga4gh:VA.KiEuI4mxuAn5Ok8q5sjrcY4oXEpIBuaX +1782 NC_000003.11:g.10188318C>T genomic True ga4gh:VA.FCZfpbZPiE8swKfwlomL9onUs-yztH8u +2427 NC_000003.11:g.10188317C>T genomic False ga4gh:VA.bnMgdcsjnZtRw_NZCD_aHwXkUd3m7jiC +1771 NC_000003.11:g.10188319del genomic True ga4gh:VA.FAQRQs9cMBQkGNhLmSnffSxzk5oFHHjK +3556 PTEN P169H protein False ga4gh:VA.io-9UNNu2Im46Qg67Sp2vQ2hyPusGGGc +2005 NC_000003.11:g.10191523del genomic False ga4gh:VA.qmsx_uaQ5n6flMd-wis2ac8PLnC1eejd +3785 TP53 P177F protein True ga4gh:VA.jXdJKYx1fIbYOlyhPXFAIbi2aIgQOZYe +3786 TP53 P177H protein True ga4gh:VA.S1OxYv2VpE3PHpS-foaSY_T-dOQzMxp8 +3784 TP53 P177S protein True ga4gh:VA.xbqH9dJY53FIoZv8lISAtFqYWDTxinVv +3299 PPP2R1A P179R protein True ga4gh:VA.cg3anKWHu0q7ZBQ_0lReDUPLT8ESpmlP +3997 BRCA1 P1812R protein False ga4gh:VA.s-4l4qvnyn9_8EQUFsbT8O818ODAdemh +402 NQO1 P187S protein True ga4gh:VA.ER-tk7mwzJfiIk0vn6Kl4zRjUfiPVL7C +4141 TP53 P190H protein False ga4gh:VA.m9Ox4Yz4lvaAJdTAS8iHuSMgnNLdwu7_ +1080 TP53 P190L protein False ga4gh:VA.LGN_eNTItni7FcSVkiQeNbsm_glKOUI9 +2064 NC_000003.11:g.10191581C>T genomic False ga4gh:VA.WmGtLEChsmT7lOSTZsubLZqhQxTUJeJq +1864 NC_000003.11:g.10191582del genomic False ga4gh:VA.ImVpuZkOOx6FPWWLInGRoaesTV_3xGkA +813 ETV6 P214L protein False ga4gh:VA.isX0uwS1_BFbK4iwe_HjxtoyPztU-gKc +4473 ARAF P216A protein False ga4gh:VA.CbUtPwvIWMGv6ig3AAE8QNbIyS95DGZH +3778 TP53 P219H protein True ga4gh:VA.e7P53kifXG1OQf6LxrLJZQzrbwSL1JwO +284 MTOR P2213S protein True ga4gh:VA.InzjPwCD2iJilxjkjxay_xzop0C9f_bi +3318 TP53 P250L protein True ga4gh:VA.zSm2a8_u2Y3gxIkBRakp-JjBCeMzSihd +2905 FGFR2 P253R protein True ga4gh:VA.58HjJl4MyXc7t4vDn1wh9a1YfrHkMa0H +850 NC_000003.11:g.10183605C>T genomic True ga4gh:VA.I9Tch3k3hmCiJR2DCiQ4IYMzskIe3dXO +1218 ERBB3 P262H protein False ga4gh:VA.gJhly3f4cFd_4kmenJ9dRvb2gIUXIHHA +3005 TP53 P278A protein False ga4gh:VA.OGJipfrrY58b-r_ziLWGB4Kz8PtoEnPd +1049 TP53 P278S protein True ga4gh:VA.fTCRV1NOmPDHd7cHg5NZs7BfWO5fR61L +4315 POLE P286H protein False ga4gh:VA.QeaJ-ncTVJ_Lu1efqBDx58DxKv-t08tj +1830 POLE P286R protein True ga4gh:VA._MtEGGEuCV1wBUk8cCyW_3q3JZ9c6GSv +3570 CCND1 P287S protein False ga4gh:VA.-j8FrzkfOTkoDNGyDFFYBse8VF-g2NF2 +3571 CCND1 P287T protein False ga4gh:VA.rLRR7bKM3rDluZdc-HbFmgLnuykszugn +367 RAC1 P29S protein True ga4gh:VA.4iWcWAV640Vvyte2A99l_no3H9yB9V0d +3266 KRAS P34R protein False ga4gh:VA.stc2B9tANHB7Y-wBun0JqeDn0kvjssLW +3289 CTCF P378L protein False ga4gh:VA.a0iY37elDQlxha15-8Q3yzxlyGK8BL0v +3602 ATXN7 P40Q protein False ga4gh:VA.6JZIpPZDOqZ2QNyivKdrZnDDo6lnVTxo +2430 NC_000003.11:g.10183650C>G genomic False ga4gh:VA.sxUUebLFwMrn4lMQwIs0wDmiKVH4Rd27 +1291 JAK1 P429S protein False ga4gh:VA.JmI5OGMj6S3YXoNqVcsT9hH6-m52Pvm0 +3603 ATXN7 P42_P43insP protein False ga4gh:VA.etd3Q8f5Ql-huPHkfML4Vj4YCYdqAvDb +1616 ABL1 P441L protein False ga4gh:VA.RJsSKpLonTmBv6O6-rjHFnwIJn1JBiB_ +3458 PIK3CA P447_L455del protein False ga4gh:VA.0zz0cv0DMTVLalzBkq9xThZ9kkjQjwLY +4478 AXIN2 P455K protein False ga4gh:VA.Ib6prrvFLdoKUvUT4b83yng75dtUJBxR +294 PIK3CA P471L protein True ga4gh:VA.9FSP2_wovjcU3vETMolG6L_bMJY3zFjV +504 TP53 P47S protein True ga4gh:VA.k1Fl51TjrMMS5iDCW0xKIGTarAbDhKwj +1623 ABL1 P480L protein False ga4gh:VA.0mZEtxmPFG5L53lpBWppzYye1JoOE2N8 +3377 CDKN2A P48L protein False ga4gh:VA.idxK7PchDa2blY86Hoa-xMepXlS9140_ +2796 BRAF P490_Q494del protein False ga4gh:VA.gNcvBg_JQP_tVFEWD_MwwAWm477SjQOe +1582 EGFR P546S protein False ga4gh:VA.JAHubf9WzI7IqMMUKduNAU7J9VhhqJYx +950 KIT P551L protein False ga4gh:VA.4S-1YbvzhrtnItNC7TQax4_ILgW43Yrr +1497 KIT P551_E554delPMYE protein True ga4gh:VA.ldL5hh4RBa16IRN4rPzVgkNZD1e43F9C +976 KIT P577L protein False ga4gh:VA.OtDQxDG8bR2AzkpnRad72T7DbU6m0CJL +862 PDGFRA P577S protein True ga4gh:VA.OL8_QBXFhzlzA9lS76GTrKNNDiMGg7wO +2738 KIT P577_D579DEL protein False ga4gh:VA.p05JYDeXWhNbaFqgcHy9f6TUU47eXboj +3489 EGFR P596L protein False ga4gh:VA.Fx3M2NXnX1h2zRLEvvCpWbOdH5a32med +1930 NC_000003.11:g.10183706C>T genomic False ga4gh:VA.wY76yNpgXWPOF0fpjjkoDDoKtPeqUuaV +851 NC_000003.11:g.10183704_10183705insC genomic True ga4gh:VA.g_N_EAcGVJmlqStIChlUxnui-DqmKUdQ +1929 NC_000003.11:g.10183707del genomic True ga4gh:VA.xIHwNGOOmP3fD2lCNKbI8FeO44dsfpyJ +1931 NC_000003.11:g.10183714C>G genomic False ga4gh:VA.ibOJ5O2H6wp_o0b9BwHoRpezzbekpSbX +2145 NC_000003.11:g.10183713_10183716del genomic True ga4gh:VA.ROooWpMrOg1GgRMPN8fwlItcNkEozfOj +2180 TSPYL1 P62S protein False ga4gh:VA.aVVO1oHwXfY2CwWDzxcWTUTQzi7Dy7gd +2990 BRCA2 P655R protein False ga4gh:VA.GHQu2OCmRjLizFiD3B9NkVDM4HLi4Lyh +531 TP53 P72R protein True ga4gh:VA.N8fUVKlEMe5Z-yQOF7kJyT0ibAQTICwn +2224 BRAF P731T protein True ga4gh:VA.VUo0eV5Bq2U8IIjG-MoDV3BptewkUHTR +460 EGFR P753S protein True ga4gh:VA.WanlFcw9OM8j8TQOqf1SzVO93bHsaCix +2217 EGFR P772_H773insH protein False ga4gh:VA.6XfBRakmQhiYbVOjBfU_tQZukhaJI7ef +1667 EGFR P772_H773insYNP protein True ga4gh:VA.wxVLFi_HD3RYcuOUZ_LZ4MgVYl6K0y1t +1668 EGFR P772_V774insPHV protein True ga4gh:VA.Hg0aAgPGtYyhH1nz8k4vdESyoE1zFIwi +2697 PAX5 P80R protein False ga4gh:VA.vycFJqJibV0BCzz4kQ3JWfpwrswJikcT +2084 NC_000003.11:g.10183773C>T genomic False ga4gh:VA.WHze5TJET-2Gz2g45ml5Jc0Z73AyYLt4 +3644 PIM1 P81S protein True ga4gh:VA.6R3H3oLKplu09WZG37skH7JI-mZAA-WQ +1837 NC_000003.11:g.10183772C>T genomic True ga4gh:VA.JyguWh_lD3Djt_BLbMmkAZvT7j4PzZiX +3384 CDKN2A P81T protein False ga4gh:VA.0F_VJzSY1ok_tAPuJJoQ_-QgkAJ2orvV +1465 EGFR P848L protein False ga4gh:VA.JdEq6bLC7WjvnO2doTOiYCnajHLmP-sD +1759 NC_000003.11:g.10183787C>G genomic True ga4gh:VA.PxYalBa-wEx_lPKrnYTd9Pdy9JIkZ6ta +2307 NC_000003.11:g.10183788C>A genomic False ga4gh:VA.MFWnnOZ5rEotVh1v67xaQwvgWZeXB64s +1760 NC_000003.11:g.10183788C>T genomic True ga4gh:VA.xELuCHVVaO4cdSnFWujC79wbDi-_dgcj +1849 NC_000003.11:g.10183788C>G genomic True ga4gh:VA.1shK7tkKU9RrJe_UhGXUXCf4wGh1qArt +1902 NC_000003.11:g.10183787C>T genomic True ga4gh:VA.J8wxeenIdvSZH1MjBCevvTzBCn1uKpsK +1758 NC_000003.11:g.10183785_10183786insC genomic True ga4gh:VA.8JRjQgJ8puLunfHk5EVnyBoZ6-32dr5X +480 DNMT3A P904L protein False ga4gh:VA.eGCEVg1OY6Cl5sHNMo83AIb240e7wcfe +3348 SPOP P94A protein False ga4gh:VA.5lK9yp6-4xfFOzIFA3hK4TF4WJXDyzxf +4304 SRSF2 P95H protein True ga4gh:VA.iqALopY4gkADar5y8WCAfm0uJVjGYG5r +3533 PTEN P95L protein False ga4gh:VA.rhcx52ta84iQl7i5uZq9oLMKfASqowmV +4303 SRSF2 P95L protein True ga4gh:VA.0B2SzZh7TRNr4slD3qdJBBl_EAmp6LbN +2117 NC_000003.11:g.10183815C>G genomic False ga4gh:VA.zbk_AvPE9AcWbjOs1N_hlGyAbyG3uSuf +3534 PTEN P96Q protein False ga4gh:VA.ciEWhNoQ_akKLDx9b0j3FOGYSd-Fj1P- +2128 NC_000003.11:g.10183822C>G genomic False ga4gh:VA.NghyBT8XBooSJLHy-jrrRwTQ-ZKlNcy4 +2069 NC_000003.11:g.10183821C>T genomic False ga4gh:VA.UVKYIgOPWRX76reBBnVEgdMO8M9GgBQx +3761 TP53 P98L protein True ga4gh:VA.1hFKBYqBxpy8rwmGghkjCC0MEbP6s_Kk +3760 TP53 P98S protein True ga4gh:VA.GOh2pOVPMZ-b3tGUw1hFjyzyqCZQGQo6 +3302 TYK2 Pro1104Ala protein False ga4gh:VA.pEbvPy2gPAXPlxwcgKtq3uwESrAq3J3O +1159 ATM Q1084* protein False ga4gh:VA.IIboH4bKZXdZZmJUN9IutBdLOmF1bPh7 +469 TSC2 Q1178* protein True ga4gh:VA.RZQfQfXPXMjLW1V2GU2r7UIqkoaYSLPw +1994 NC_000003.11:g.10188251C>T genomic True ga4gh:VA.mt8Ys0jGFjQy-2Ro2cEVfGCSzjPd6LMK +1882 3-10188252-A-C genomic False ga4gh:VA.NSW0pHgSTBsMDdvgAzCh5rY2GJTkTUfr +2125 NC_000003.11:g.10188252A>C genomic True ga4gh:VA.NSW0pHgSTBsMDdvgAzCh5rY2GJTkTUfr +260 ABCG2 Q141K protein True ga4gh:VA.IYFc25HMx_KFYhRP7FsVOAjq1p70p2A- +3777 TP53 Q144P protein True ga4gh:VA.et4V5nugHJ8o91HdfbgdEEuGW94krlov +4132 TP53 Q144Q protein False ga4gh:VA.s5TK2rD8ahj5OURgzarqwPvxB2k5McI4 +1883 NC_000003.11:g.10188290C>T genomic True ga4gh:VA.s3x4KLTSCRDIyQuRbHpBFOYEScgcfRS0 +1781 NC_000003.11:g.10188292_10188293delGC genomic False ga4gh:VA.oGMVszzqhVSwzCW3aZeRbK4tllXSHWYD +1246 BRCA1 Q1467* protein True ga4gh:VA.0JVFFE62MXEmlYXaW9akLmjoN6NZptV2 +753 MLH1 Q149* protein True ga4gh:VA.Tja6Cn9WuAyE6JAKczBiktBWQTOsrBWT +1845 NC_000003.11:g.10191497C>T genomic True ga4gh:VA.lB8t9LNu_lJoJLu9rwQwFNAn3obS9-LU +1943 3-10191499-G-C genomic False ga4gh:VA.Wbaxdh6rfJe2V251Uc5MuDFs-B2TOyTm +2880 NC_000003.11:g.10191499G>T genomic False ga4gh:VA.zXbG09rRDdkfrdxwvNX_fj80g97-4Wvr +2079 NC_000003.11:g.10191498A>T genomic True ga4gh:VA.W9SZ5sOjfWK2nwh7L1h3otv2bovOMqS3 +1856 NC_000003.11:g.10191498A>G genomic True ga4gh:VA.86ArciKhgTCgVO35WlSIEAbu5iNnoxS- +4135 TP53 Q167R protein False ga4gh:VA.rutoyargusNJzBIcvYME5o1OOkwAOl-c +1654 NRAS Q179X protein True ga4gh:VA.BIM7j5rbQRX20VGuA46LzUjvKP_0EYxc +1593 PTCH1 Q17X protein False ga4gh:VA.ykbATdum-HnTxICnaBy1SZ8aOEfjrn67 +1810 NC_000003.11:g.10191590C>T genomic True ga4gh:VA.s5QixZpydwXdMn_RrpuJDyRNMBLzm4Gc +4413 GNA11 Q209L protein True ga4gh:VA.LKPI4Zf_or88V1pz08V7Msk0Xj9wSwcj +604 GNAQ Q209P protein True ga4gh:VA.dbFA9k7iKP_tLm-hOdXyGE7kVy7YMLm1 +479 KRAS Q22* protein True ga4gh:VA.u8GdPKKJEO8p6M8QafMcQiuaMU8xJqL3 +1520 MTOR Q2223K protein False ga4gh:VA.P00Ito30yEkRhD2rSOfdj2ujCUJrLIFm +3601 ATXN7 Q30R protein False ga4gh:VA.LvhSfaAjOEsefwnMsf0rsDeHLi5qNqTp +261 XRCC1 Q399R protein True ga4gh:VA.rAQ6flHbj6kdoY-FQ4113VON0uI52b4x +3600 ATXN7 Q39P protein False ga4gh:VA.UjSXoc8Mf7NR24vnRdGtJkiE5uCUoyGk +3590 RIT1 Q40L protein False ga4gh:VA.UO1Ym5JLQwTEYJRfdC69lOILYPApBFQ3 +1510 ARID1A Q456* protein True ga4gh:VA.GF_QlrYVPx9DffkDADt2Wy6EyfkkUJUS +1564 SMO Q477E protein False ga4gh:VA.Wk8Xog1puKxLJhmEd8K5RJ0TkI5AoMYF +614 JAK1 Q503* protein True ga4gh:VA.vV4laGcMnfnFCIUoYp2dp7zNb4ohxEIK +3663 BRAF Q524L protein False ga4gh:VA.pz_SC-5lsXraR50QBk8s5Y1ZIYOfTeA3 +886 PIK3CA Q546E protein False ga4gh:VA.bEoqf8XBjrAyF6vHVb4UHG4XgQVaUOlh +885 PIK3CA Q546K protein True ga4gh:VA._TDbkBGDlBX6EfTuxt2Jv-9QUXwEQzUv +887 PIK3CA Q546P protein False ga4gh:VA.VPvxvpuRJLzumtDG26vGWgFgcf8MOEk6 +888 PIK3CA Q546R protein False ga4gh:VA.uNYg2GvPgLO19kJSkboPZvgCadJpvSoP +1541 KIT Q556_I571DEL protein False ga4gh:VA.WfL8RORBMoCjSu1nROeIDCo3vHYK1RVE +83 MAP2K1 Q56P protein True ga4gh:VA.Tkb5vESjzbd7eUDOsmfUlhmg-TJTQM7g +655 MAP2K1 Q56_V60del protein True ga4gh:VA.-dSI9zjt6Th-k0ciIdCDsQS572qK24sj +975 KIT Q575L protein False ga4gh:VA.gnmn-ZzyNClhTwbm_17DXFc42TveDB3l +1104 KRAS Q61E protein False ga4gh:VA.6ijlEIjCKevOfCPV6GCDcRmPkSy-L8E- +893 NRAS Q61H protein True ga4gh:VA.qPk_A1ivYE7HIKO5GasYeFbzPT_w6drG +907 KRAS Q61H protein True ga4gh:VA.4IR2386_BqFwulwfRUoodJKWVgWsImJl +427 NRAS Q61K protein True ga4gh:VA.wGJ5e7pU6y670rqWxnIeJEYZeQnjXX7M +910 KRAS Q61K protein True ga4gh:VA.7rInaAjpNpzTclj6L_ddyvqtr_iUheSm +1392 HRAS Q61K protein False ga4gh:VA.WcDrlD3oTJIpd7DpbxjIg7p_xPWgP5fz +95 NRAS Q61L protein True ga4gh:VA.5O7aEDzcl7FhKsqeg5WT_iirqIjCpHTr +854 HRAS Q61L protein False ga4gh:VA.6UyqPWnDmVC4-pcRRaS54zcSzwzSpTZ- +908 KRAS Q61L protein True ga4gh:VA.d7EkBJXk9OLCZpvoKrYbKT1MRl7j48jv +1103 KRAS Q61P protein False ga4gh:VA.0D8TCKiigqU5rdI_cK6GWI6nBIq8VihH +96 NRAS Q61R protein True ga4gh:VA.UtLI1rrsdnYpKO9B6xHJBsUHmJ6tRrYn +909 KRAS Q61R protein True ga4gh:VA.wHoRx8OrImYp4HSKFlCnXz1CU75XWksK +1391 HRAS Q61R protein False ga4gh:VA.EkM_Y0QOWAgQWQTQSwJNT8CzJ4D59dL0 +981 KIT Q694K protein False ga4gh:VA.1bvVZ3VGvx16Tnp2wfW15aIkIbU7Y2sX +3576 ERBB2 Q709L protein False ga4gh:VA.wMp9pcZxdItt4MBhXNzT54tnNnH8-z1l +3433 RRAS2 Q72L protein False ga4gh:VA.xbFB4rHN858D8JVa6kM7dspc75RLZ5il +1752 NC_000003.11:g.10183748C>T genomic True ga4gh:VA.jxU09CoBMwwehEhSzXkbSEUHab9cOgtR +2041 NC_000003.11:g.10183748del genomic True ga4gh:VA.Ratf26VR1Ceq1s5IY-3bFpUMdXcdhDt5 +1592 PTCH1 Q787X protein False ga4gh:VA.UkeQSyZKB4DE7bG9nMfhSzNq9HENdoCW +169 AKT1 Q79K protein True ga4gh:VA.Pe43JRYv1WflN9WDZMLixfKaWmF6G9fI +3589 RIT1 Q79L protein False ga4gh:VA.Tv37tDuzw0qVeIa9eVI8xpWNGxK5BRQK +1848 NC_000003.11:g.10183817C>T genomic True ga4gh:VA.XRslar74KA6_nYtQ0bAKCCvex6GJGm0x +1818 NC_000003.11:g.10183818A>C genomic False ga4gh:VA.5-B74dGd5c4bK84xoKaim9XmqghcTExQ +3246 NC_000003.12:g.10142135_10142137del genomic True ga4gh:VA.7tXGPYPzBTuiHs1HcEVg6Hfg2AjMJNK9 +1157 ATM Q984E protein False ga4gh:VA.2UaLuGk_0dIGVrOOCw1Z9UxZvQx166bS +741 MLH1 R100* protein True ga4gh:VA.qRZC3yrDgrTJdmaU_E6Qu6p-L0X50xdn +2774 MET R1004G protein True ga4gh:VA.u_JFmVudO1pHQYSSwXk6r6kFqz7rZBsO +3653 KDR R1022Q protein False ga4gh:VA.riCZdzKRDX2W8GboLmHS5RqCXiDDijHg +1594 PIK3CA R1023Q protein False ga4gh:VA.Ym3zOPL8Ql2Jy2gbNlKyMrVf4C3fNZyr +3350 KDR R1032Q protein True ga4gh:VA._2vfO4U7rnY2ux9W9vwNtUBma3xVFvJ0 +702 ERBB3 R103G protein True ga4gh:VA.ppv3hMnisO3rxkROO0Xn-pi3M-XU0Vwi +714 TSC1 R1062W protein True ga4gh:VA.M6jEnjG4-TXDToR5gNwnRowrsil7OHfI +2007 NC_000003.11:g.10183850C>G genomic True ga4gh:VA.Wq1zc1_X12ze3K6GE_hRuSlYx7Gfzbge +2044 NC_000003.11:g.10183851G>A genomic True ga4gh:VA.m7jeqzW3TVK_5VN1B2oO2WZLzCJSVzgk +1840 NC_000003.11:g.10183851G>C genomic True ga4gh:VA.qsEBa_rvv1JABdmSz_50hDd1w6nKT9YH +994 EGFR R108K protein True ga4gh:VA.tNmIY-gbjtvbdGRmjiCJbaTRS2IuWnwt +3282 TP53 R110L protein False ga4gh:VA.2dBLkVBr4mBfuyPUlsaG4ivBByt2Ihqb +1796 NC_000003.11:g.10183868C>T genomic True ga4gh:VA.9AlWpZOOakQ5UvYRXtf8uKw2Yv0F2zo8 +2143 NC_000003.11:g.10183868delC genomic True ga4gh:VA.71hcpXH-cZEoXE4ajvMU2tLQijcYJFwg +4318 SMARCA2 R1159Q protein True ga4gh:VA.ENjonuU1V7xHBLe7XFtV-KcW7xLoBJM2 +1661 ALK R1192P protein False ga4gh:VA.5EaT0Wihx_hOGhBDiv6BKOwB7P-C_TP- +2877 3-10188215-A-T genomic False ga4gh:VA.zqw2H1hhIs8eW8LHQAZN8bNOXU3NiD-r +3498 ERBB3 R1202W protein False ga4gh:VA.GC-Bg8ynoXpF-dC9SkkR_1a0HeOwqIkp +1914 NC_000003.11:g.10188215A>G genomic True ga4gh:VA.qOqTQfIyd6BmAziD_vmzHKVxqNhkKSAq +2494 3-10188216-G-C genomic False ga4gh:VA.3uZOJP76aCQxyOti4x61236oMzJODOYN +3244 NC_000003.12:g.10146531_10146532insAC genomic True ga4gh:VA.qLkrdcLNMjGeXRbRQo1LzSk7tFWzzSht +2645 KDM6A R1213* protein False ga4gh:VA.S0RzRszP64Vdd78W8cm7VdQ69ogza3iX +3300 SPOP R121Q protein False ga4gh:VA.6EVJLNBNOhWgCqZASNxURFMJYj9rYvGL +776 MSH6 R1242C protein True ga4gh:VA.-GKJXnUYYvtFwQPGHmEOdM9ykjfWYT_Y +767 MSH6 R1242H protein True ga4gh:VA.7qlVnF8_OMCpL9geEp5ZrlTI_EbM-174 +9 ALK R1275Q protein True ga4gh:VA.-RMKK0gYsa7YhZsuDpGPTnZiXCejHm1P +3292 NF1 R1276Q protein False ga4gh:VA.9tBPK8QXcG4es84MQ_ypTbVCq1-VQXhP +3060 BCL2 R129L protein False ga4gh:VA.cQxbHAbH5eYluqaVRwGcY9tbx7hmeoIr +636 PTEN R130* protein True ga4gh:VA.NxUwg2XnX4ZdYxO-7h0cvJ4gedCvJ0K5 +1037 PTEN R130G protein False ga4gh:VA.SzsT89Vqap4vx7VcCIfWvQAgaWmC7bYF +899 PTEN R130Q protein False ga4gh:VA.KNQU2GQla5dODeFxMYhM_je91vAhmkUv +59 IDH1 R132C protein True ga4gh:VA.O8zC-ad_EKRCy_aO0XPs5spF0sEYDsU0 +927 IDH1 R132G protein False ga4gh:VA.nB9f7uL9HBJj70ZqSimBFCEwv_1W0KMC +420 IDH1 R132H protein True ga4gh:VA.iZh-igOaUaWlGiz1m3WbZUVvwDyLEJ4R +880 IDH1 R132L protein False ga4gh:VA.My7Dz91of1BesZ9PVk5u_vovguNywRCr +4433 IDH1 R132Q protein False ga4gh:VA.WSww5PoknaPfaOc_UNG4NgAnPSSb5l7f +928 IDH1 R132S protein False ga4gh:VA.jNPuoVr44MWaWXmffeUgLdN9lxYisgaa +4102 TP53 R156H protein True ga4gh:VA.uAThlQE5tIvfpIRx5VpahXyJWLE9Uulp +3795 TP53 R156P protein True ga4gh:VA.rETDV0FduqHvy0cEP3atmFi7zIKDRVX4 +1170 ATM R1575H protein False ga4gh:VA.Vun8Qw62AwgfVtFTn9ZWFwUtQMMzeFEW +3967 BRCA1 R1589P protein False ga4gh:VA.VNzUl7ojCveIRSV8pbT18RzhnXFsLhPW +4133 TP53 R158C protein False ga4gh:VA.I1rkvhYI7UESicqhGGxgiA_8JbOl1FdG +4115 TP53 R158G protein True ga4gh:VA.h02alGZQu5GkOs58dzkntiKJxOokSzrG +1695 TP53 R158H protein True ga4gh:VA.wCQZbgdlV34gsjjqmdF--myPTvan0KCD +1699 TP53 R158L protein True ga4gh:VA.kOw5LU2mKSKplgaD9JHIvm4bpL8QPe9m +3543 PTEN R15K protein False ga4gh:VA.SZwZKRFGs8VG0FT_2JQw9VcAVkRRTAoD +1804 NC_000003.11:g.10191488C>T genomic True ga4gh:VA.UAK4bN5r0bGXcbZYNHGrmx8Fmq2EeUv5 +2148 NC_000003.11:g.10191488C>A genomic True ga4gh:VA.CZf4CWbNMYtMJd7BAccaDafTIzludE1c +1915 NC_000003.11:g.10191488C>G genomic True ga4gh:VA.EO3GK9IkiXWbH07hQWNxDcKaUu6fVoz7 +1855 NC_000003.11:g.10191489G>C genomic True ga4gh:VA.Br4shs9Bzm7LJTBEkDw9l7LzAvZi8ZKR +1746 NC_000003.11:g.10191489G>A genomic True ga4gh:VA.17D2LbK70vqbCtqPAtV-WgdMsHo32YT0 +1628 NF1 R163X protein False ga4gh:VA.11mAAxSS0WaTJHw_owd1NVJqv9ARgGKU +1207 KRAS R164Q protein True ga4gh:VA.tB6I_7VCKZqLceE9SIm3pvP8fjh38LO_ +814 DDX41 R164W protein True ga4gh:VA.fzz9qQ3rCdpbVwQeSSIOlVsUzrsdjfmF +3470 EGFR R165Q protein False ga4gh:VA.D5gNpSOZHd3AV5qIwYL4-D50iATDnLtX +1805 NC_000003.11:g.10191506C>G genomic False ga4gh:VA.kpLrfmZV7r9TBwrQi8boquuFrUZ9gNGx +1916 NC_000003.11:g.10191507G>T genomic True ga4gh:VA.U75XvIxkGVKILHF-xhqQOW2AG8sRuMOC +2458 NC_000003.11:g.10191507G>C genomic True ga4gh:VA.9ETz4DfXNW7eT1vCCSVFVchP7MBnHjKp +1739 NC_000003.11:g.10191507G>A genomic True ga4gh:VA.6hWDhRLk-jvPmw26PDdiZE86PMk3uPfm +1747 NC_000003.11:g.10191506C>T genomic True ga4gh:VA.NgsD_748cpj4qiLpiLF1w-5xNkA2UJDL +4397 BRCA1 R1699Q protein False ga4gh:VA.lIIKhjeTGfjgwvE1EcFog-5oZ6ARCRwt +3971 BRCA1 R1699W protein False ga4gh:VA.L6gJL27_oOaQGhr2q5M8lKpdlF1_svYn +2364 PREX2 R172I protein True ga4gh:VA.1xHQvTvEzXvsN9wp0XYJkjDa9a2ONzig +63 IDH2 R172K protein True ga4gh:VA.FRHhQf23W6IpLwB95kjW5e_3QRmJzaG2 +838 PTEN R173C protein True ga4gh:VA.li8IBTtyWzVIwfqMwhbp3AxQGtl6ZCOE +3420 TP53 R174K protein False ga4gh:VA.kTHu2imjBvCgB4nsLig7J_R0UTulbCpT +1085 TP53 R174W protein False ga4gh:VA.lY-PJPNjx0Jk25r8rrNUDpyIdiZjiAcY +116 TP53 R175H protein True ga4gh:VA.kA5QYiYqxEOopJ5IwdA6j7hqdmLlDDgb +1780 NC_000003.11:g.10191533del genomic True ga4gh:VA.H4I6WdjFH_0JsE1JsoXvfuxNJjC3u357 +1827 NC_000003.11:g.10191536A>T genomic True ga4gh:VA.3S5iQcL72z0I2aIczrXeERitpM6jXtOn +1907 NC_000003.11:g.10191535del genomic True ga4gh:VA.EeecPP4BonW-BxPbT65qmbkeZkAHhu8p +3796 TP53 R181C protein True ga4gh:VA.urpU6yF8um_6Z_VY0uKUS08P4x67a0EI +3797 TP53 R181G protein True ga4gh:VA.swiU4uktuv3JmZMnrDTPHNJfj2PTa8mt +3798 TP53 R181H protein True ga4gh:VA.fMNd-VQELcm5Rlj9roeXrvG_CkwGI-GP +4140 TP53 R181L protein False ga4gh:VA.yAppW9yzP4e_L8i3EHF5tk9OEv1dCD16 +3390 TP53 R181P protein True ga4gh:VA.A_qEWhX4gNaRpkryajbb3iWGrEIyG5u1 +4412 GNA11 R183C protein True ga4gh:VA.mFzVl0B9xtuy7YHspOciMKfbleNcCu9F +471 RAD51D R186* protein True ga4gh:VA.xVlJw5zsFVC0-8ed_SlZ3-c6FAeX5KQH +249 XRCC1 R194W protein True ga4gh:VA.PR25RCsDWHsH27V78hW5_atwRGOlELfB +4142 TP53 R196Q protein False ga4gh:VA.bt2n_JAfMLpSviSn2tMc583cV0MSnByX +631 NC_000003.11:g.10191605C>T genomic True ga4gh:VA.bsHkOZhAE1xDFpjqUMEG6XKaeOKv0zAZ +826 GNAS R201C protein True ga4gh:VA.pQfIL9jK5FNTLwJWmI3eMXq1n2s0vCNJ +1319 GNAS R201H protein True ga4gh:VA.AJDDVpYn-pWkF2U2xoo-gwnQkuuKJZIU +4305 CIC R201W protein False ga4gh:VA.xY9GiEjBhrdf_6R8jgDyuGZLeTBhPrIY +2857 ROS1 R2033N protein False ga4gh:VA.jCaVepTMAnlHYgWtnDIR8CcbSwJJ5PoO +1161 ATM R2034P protein False ga4gh:VA.xWzAcCq0t-FzhiK2ruhwaW8XO4iFaV3E +3661 ACVR1 R206H protein True ga4gh:VA.L8Mx0x4W2MZkCUl86hruk6JCgoHPmW69 +3575 PMS2 R20Q protein False ga4gh:VA.YFoKeQ7kmcXmEteIz1RNZKTvK5ApYMkd +2711 TP53 R213* protein False ga4gh:VA.0-_aap-NGR-p9z2ea9k2SUMjAQ5vPnc7 +1109 TP53 R213P protein True ga4gh:VA.i0p8PU6crwnNte81pT92ZHg84h5vFNnd +4121 TP53 R213Q protein False ga4gh:VA.e58lOUxMDERCvyCmIV5s36vWqDaBIhc2 +1683 ALK R214H protein False ga4gh:VA.bG6LnOVCJg860V9t2qWlJqLWp8G8fHOm +3439 MTOR R2152C protein False ga4gh:VA.YZxM5jVUFBGn9Gbp53NpvsC3feOvKpLz +3431 CIC R215W protein False ga4gh:VA.QZ0Q6TfYP1Yz4D8pXVnL-96H99U5Qi3w +3344 EGFR R222C protein True ga4gh:VA.4GKZ1DOzgRB5BJManOUNoTZszkoTBWbD +754 MLH1 R226* protein True ga4gh:VA.0rw4SF1KNbmnPrbSzVSCMMxeiP1qJiDh +136 NOTCH1 R2327W protein True ga4gh:VA.Rpscxu1Mnetdm4VjBn-x_HDCkIg0Bc_t +110 PTEN R233* protein True ga4gh:VA.R7lzW65WVU9D5Ljmecm3V1Xb_lIWNWLc +1252 BRCA2 R2336P protein True ga4gh:VA.jIAzEhtZXfBRVDwo3aYvhSOgLwSHFx7M +2896 NT5C2 R238W protein True ga4gh:VA.DZbQ4JwzHnlDdS20moF1Rh5c8DVEhKuz +1156 ATM R2459C protein False ga4gh:VA.XxkWkPmQuoJ5vVCXuo5ntX1DBICcssNX +2403 FGFR3 R248C protein True ga4gh:VA.Ef_9GdbuoBbTePILS-NaQJn-_NhrdpoO +920 TP53 R248L protein False ga4gh:VA.6uCe4yOEYte-4jZlIHbmE6qXN1-Hp08s +117 TP53 R248Q protein True ga4gh:VA.pyQugr6PsdGYiyJckUb5MzY0bcBARvmj +118 TP53 R248W protein True ga4gh:VA.YEt-lFmCTXWedDDWCFPeU-qqsRUaC0el +3400 TP53 R249G protein False ga4gh:VA.EPvg6l2LtDJJ7M1Y2cV2V7zZy9kUUXPa +1696 TP53 R249S protein True ga4gh:VA.RH1Xl4CCKa3nkn26yH4HbFQLqRGvCC0- +556 CDK4 R24C protein True ga4gh:VA.pGp4xvF-l5e4jxY6bMudr6gyWseaiWZ0 +3961 EGFR R252C protein False ga4gh:VA.PsmNfzXYrU61f3qS5QR1EUO7jJvlwfv- +2275 ACVR1 R258G protein False ga4gh:VA.t8WEyogTSnNlSb97-6ncMhPLn4_i4nQd +3618 BRCA2 R2659G protein False ga4gh:VA.klDtiyX-Wgd58DjqaIjUmzAEjfe_a2fQ +749 MLH1 R265G protein True ga4gh:VA.udX8ZQnEKf2jmOl6PuXoPivtu7kKHzLk +3421 TP53 R267Q protein False ga4gh:VA.SfZ_b06FzTzACsS_VFD85GEASf9uvg0j +121 TP53 R273C protein True ga4gh:VA.MlbeTcUAPVhmYx8KZKtTuvG8WcCUjO4O +122 TP53 R273H protein True ga4gh:VA.kcPAoam8e66opWWbjcHmCNQ7DbgOV1Uq +918 TP53 R273L protein True ga4gh:VA.GdTME3rpcPjYk8OSJK8f056eXIyQ5E5H +2753 PRKN R275W protein False ga4gh:VA.xC3KNHtKR1fO4XMaRQkjiER26lm38UJN +3619 BRCA2 R2784Q protein False ga4gh:VA.1bK0LWvZoHC6PfMCvbjiaY_D6GJyFHRx +3626 BRCA2 R2784W protein False ga4gh:VA.y5jOXlhVMn4r-Oc8Vj8ilFzEejd7YpsA +1697 TP53 R280K protein True ga4gh:VA.90Ig1Xn0etLHs4dLsmgM33djKUUGaT4k +1698 TP53 R280T protein True ga4gh:VA.TzPrzxNVLWjVpPeWp9Iu_gbuIIcN8qqm +1108 TP53 R282L protein True ga4gh:VA.tOqFETsCpKMy-EzShEo6abFnaLS7IOTB +916 TP53 R282W protein True ga4gh:VA.dtMsc7k5w7YqCrcXGUNf9e7CEBiZH8Hh +3799 TP53 R283H protein True ga4gh:VA.owKcgjsuIXsXdFx0hrh65z_3O13YzoFP +3422 TP53 R283P protein False ga4gh:VA.JEoX3O_rvk12f41bGgtQYWNbDXaOHwaZ +3608 BRCA2 R2842C protein False ga4gh:VA.OOZz2_ww8yZSOFJjvU-qU7tDqjTQLXGd +903 ATM R3008C protein True ga4gh:VA.Y9GGlMzdtG-ORDMbQHA5psnFegenJxIo +4148 TP53 R306E protein False ga4gh:VA.MnT0cgZMeaTLKbA-UW8yW4gJevcvdLsm +768 PMS2 R315* protein True ga4gh:VA.hINmeJ7MIq33czNuVxhc7BkK5TiobabI +3423 TP53 R337C protein False ga4gh:VA.UV5uBQwAS961ajhCiB18NWuC1wBUm70n +3424 TP53 R337H protein False ga4gh:VA.7eAs8-daVG-1ckVaVkQtG2jQJzrYhMer +1112 TP53 R337L protein False ga4gh:VA.qI8f_EfncWamtYNHqDFYl6eKsl7loSS_ +3582 TP53 R337P protein True ga4gh:VA.-yQ2bEJ1SDsX0a2LwwxQdHFkDKwj4TtS +4149 TP53 R337S protein False ga4gh:VA.lyaf5xYn8Jft0XQmSjl1UclPcJxH43aa +3579 TP53 R342P protein True ga4gh:VA.PxKG8J3mFdEHRnAK5Pdqt0ZglXiK8Bv_ +1656 ABL1 R351W protein True ga4gh:VA.tk0x7TzafAzf4d1beMH0_Ycn7SJTP_dT +2276 AMER1 R358X protein False ga4gh:VA.fivKZTi0H7q3KPWzYSjmNVTtUymsQkCk +2851 SMAD4 R361C protein True ga4gh:VA.DDC3Jx9Jbeac1Qsjq_NY4Jybgj3t_gu3 +238 NT5C2 R367Q protein True ga4gh:VA.Inp_jWvckmfJOR7aDKuju9jYL6OwTTrD +812 ETV6 R369Q protein False ga4gh:VA.TG6R-i9ZC4W-u1P-jKxzXlii8Qg5gsmZ +3757 SMAD3 R373H protein False ga4gh:VA.ViocQdeeKxRKlQSkBYMO5lm7l1vSVZAY +3339 CTCF R377H protein False ga4gh:VA.wS3BU9J5QpqzQWUe4ddS0ahHOBAsETHQ +727 MSH2 R383* protein True ga4gh:VA.xUuVdx_GLO59fLdxUPKc6kXOqMj34M2N +1680 RAF1 R391W protein True ga4gh:VA.aIA7IJs39BvOUBoeD0hVY6k99gpRB-Aa +811 ETV6 R399C protein False ga4gh:VA.-KcMILg347ADBaheg_JD5wG-8htBp5kf +3463 PALB2 R414X protein False ga4gh:VA.VMTArR0SKx7llY9tb7jxERpoQdULkf-O +3678 ETV6 R418G protein False ga4gh:VA.Mw406RNLc3PpTMeC8q8CAVQF0HxsgRXE +454 EGFR R451C protein True ga4gh:VA.VlJIX4VF0CNM4dzVoHIrqKkxS5jmDKJ4 +3144 NTRK2 R458G protein False ga4gh:VA.vFKuNURMPk9gHU8Nmk72d6hNZyUudO0m +3671 FBXW7 R465C protein False ga4gh:VA.GBY27q5MjlsyHpu5DwjRksTzKudwZuqp +2647 FBXW7 R465H protein False ga4gh:VA.eXbOxpXZvxtNyruiGoF-JU8Hx132Ulxb +3672 FBXW7 R479Q protein False ga4gh:VA.9HnSRqH8dO4tqBYlHLZtq2_3ps7C3wP- +3519 SMAD4 R496H protein False ga4gh:VA.4gI7kPqrwpPDOwgscPAAtn4Yo15BucRM +1503 FBXW7 R505C protein False ga4gh:VA.V9RNAExMjNOOyDH1j-sW-l5ksZr9RkD2 +1504 FBXW7 R505H protein False ga4gh:VA.1HcZINDO9h-K9QtQA07ZxJ9rtxqXrk_1 +3673 FBXW7 R505L protein False ga4gh:VA.g-kjEDrmPG1kgmvMXmmJgakmFYnwleSR +2803 BRAF R558Q protein False ga4gh:VA.fiIXRLzszJnngACs2f9jxzR5g5Ds2qzx +2302 NC_000003.11:g.10183709_10183710del genomic False ga4gh:VA.mTNad8iR-5e717ZCaNz5-Q-Yitv4lDs8 +1867 NC_000003.11:g.10183722G>C genomic True ga4gh:VA.YkTDNQ9QJIrNSEerg0YiBo_h7OC3_Rc7 +1679 FBXW7 R658Q protein False ga4gh:VA.bH4ZfBfHCCwU4zS-MkUysGJAiw19C4HF +3696 FGFR3 R669G protein False ga4gh:VA.6tFkOdnfgO2hP2eeaCJD1f84YLAiZVX1 +3697 FGFR3 R669Q protein False ga4gh:VA.cgTUDAohXqHBubbExHCDNu9fv4JH8e85 +42 ERBB2 R678Q protein True ga4gh:VA.Qq-mYH3c4oxVeJHs-G2eMRd03wpH3Q3E +2829 JAK2 R683G protein False ga4gh:VA.AD31wqS7JQHC7ylFn9_y_u76arSHOam8 +3604 EZH2 R690C protein False ga4gh:VA.9jhGes7ebjZwSJKTqyb1Ya-dJ5ia4ms3 +2333 EGFR R705K protein True ga4gh:VA.GqkCIbW_lV-XC3vbNC9UvMvB_jq3Bw-t +4404 CDH1 R732Q protein False ga4gh:VA.viUzmcqv-jbzLA5GtGwWk6YyTfDzje2q +3485 DNMT3A R736H protein False ga4gh:VA.eS6y-GLz8gbjzUlkw4DFVWfmKkc5iFKR +1181 EGFR R776C protein True ga4gh:VA.VlhRRbg95kN2-NYSLCkqxn1jUWQogUlE +2175 NC_000003.11:g.10183766C>T genomic False ga4gh:VA.RdZHD2OpQXUp8pXSmTSnpsQlIzrwX4sO +1791 NC_000003.11:g.10183767G>C genomic True ga4gh:VA.-4KGs7zAWhi2h7xAeGiTDQ8IQqA4PCiK +2241 NC_000003.11:g.10183775C>T genomic False ga4gh:VA.PcIpmEHm0A1oG-Ol8cOoCckWohxeqZ6E +2532 NC_000003.11:g.10183775C>G genomic False ga4gh:VA.Ya9M52GKtcdTBTCrkP00GBLacTsMSqM1 +2110 NC_000003.11:g.10183776G>T genomic False ga4gh:VA.BX4d7rw6MplHxsOxGeJCzczMoy77KCMA +1980 NC_000003.11:g.10183776G>C genomic True ga4gh:VA.1t7zFZqfvQQMmS7uRto5oIsZqlk_aQ6O +2089 NC_000003.11:g.10183774_10183782del genomic True ga4gh:VA.VmrBrfTfdXXLfpAM_ikWBRyti-ECqfAU +1017 EGFR R831H protein True ga4gh:VA.xYpGKIu58-HlholzrXShE3kImUQq50OB +2741 EGFR R832L protein False ga4gh:VA.BswwdDkJeRK6ir6Un8RYRn-sm-Q-wJsf +863 PDGFRA R841K protein True ga4gh:VA.UGHo6fT7nAwpsqyLhqYa1FJSfC9r3QQ1 +2782 TEK R849W protein False ga4gh:VA.Yg2uRKHJEjXETAJCQlytqn31vfkhezaF +3376 CDKN2A R87P protein False ga4gh:VA.rsAkmUlAVxpvVQzM_4OlpEYFXovCR5aA +1125 DNMT3A R882H protein False ga4gh:VA.EPhBezYC3g3EoxzsMN_xcmt4-YZgSwkc +1124 DNMT3A R882P protein False ga4gh:VA.yTbzcMdQPLASP-ajZ5l2PZ0h5b8_jQ3X +929 PIK3CA R88Q protein True ga4gh:VA.9TmCiEAS0L-52bAUMQnXzVITRFBt7m_1 +43 ERBB2 R896C protein True ga4gh:VA.kvnRskmrX2TomwKvfxj0QeZoWQ6zdn9l +3434 PIK3CA R93Q protein False ga4gh:VA.xb9_5LtecqimcOpGYC3KNzbfon9aESHa +1178 PIK3CA R93W protein True ga4gh:VA.wHztQ_efD7jQU0Y8msRfIayrV-TYBVul +502 KDR R961W protein True ga4gh:VA.FttsZp7xmlF3ySA_5l_7syggGY4ePD-K +2790 PIK3CA R975S protein False ga4gh:VA.JvvC1LIH7VAirfC3-SYqm1cqdMjNnDdQ +3685 PTPRD R995C protein False ga4gh:VA.9Me6tnxYjKT7G8MbgKyyfmaOyXx5xX01 +3429 ARHGAP35 R997* protein False ga4gh:VA.9waI-yAvs41gmPQ6DQgGRpVcRzAeHnOd +2925 PRPS1 S103I protein True ga4gh:VA.tGwsg_MsP3RHGkRhjTXysaIEMNruGdPk +2926 PRPS1 S103N protein True ga4gh:VA.2U-p8QDOjrcZf8U7hzs9w_Jke5PCRcgZ +2927 PRPS1 S103T protein True ga4gh:VA.rZvbpHpQs5hyBP6DYKPBVhk1z0f5cc9T +3497 ERBB2 S1050L protein False ga4gh:VA.e75CreaYtCchK-SDeKQ-X4NWiaUyIASO +2165 FANCA S1088F protein False ga4gh:VA.TXQrPzKNc-fnYG0MEMQxJTmS34XlkPGB +3647 KDR S1100F protein False ga4gh:VA.0Y8XexpuaN8OPX3n5XVOV3gdzL1LAicO +1853 NC_000003.11:g.10183861_10183862delinsTT genomic True ga4gh:VA.YLj6DzYmRtlcATLQasC8mmbAu61AIn8X +2045 NC_000003.11:g.10183862A>T genomic True ga4gh:VA.6pWoOZq_4jKbjbK7giSUfH1txibYxsve +1762 NC_000003.12:g.10142178del genomic True ga4gh:VA.zBn1uqInBLPdRbmseBhV3YzgKym-cRXU +2243 NC_000003.11:g.10183862A>G genomic False ga4gh:VA.SrTprzGXQBOKyk8ip3ZOufkz6ioPoOVo +1763 NC_000003.11:g.10183863G>A genomic True ga4gh:VA.4CLBIryajVGVY9kOTxIH6e4xYXdtjHP6 +2156 NC_000003.11:g.10183862A>C genomic False ga4gh:VA.pKE4ygk6CBXE-WgdHp0vLkdH3ovIN1z_ +2003 NC_000003.11:g.10183864C>A genomic False ga4gh:VA.I7wD8XqOVhVgET9aSy8DmZCTARHGveRV +1764 NC_000003.11:g.10183864C>G genomic True ga4gh:VA.FqIQkCMO9PBE7UZ8bXh0tz22itT2bgRX +2517 NC_000003.11:g.10183863del genomic False ga4gh:VA.LrfvQ_y_xM4BRm7dmHaUrrXQ8rF_Loqc +4333 ALK S1206R protein False ga4gh:VA.rPNEPBc1B9NuH7Y03d73rdU7JcPl96m- +172 ALK S1206Y protein True ga4gh:VA.3zaL4c_h9jsZJmXjCeO1he6URh1D0rqs +4130 TP53 S127Y protein False ga4gh:VA.fgstS9Z7eRO8YnEY18ERf95LrUOSMa1p +2541 NC_000003.11:g.10188273C>T genomic False ga4gh:VA.VQoj4WnCE4Iu0QmBYoGxm-JbWxjOnAB_ +3969 BRCA1 S1486C protein False ga4gh:VA.WLnhOWU4KscYZTp7Sl-YWdLQTgsRU3WR +1499 PIK3CA S158L protein True ga4gh:VA.7hSY1T8cmK1KTUVlW99NC7n1YVjp7QB0 +3964 BRCA1 S1655F protein False ga4gh:VA.wFchplQRVijvcVB-dUCPZCOXLa-FV7SN +2004 NC_000003.11:g.10191510delG genomic False ga4gh:VA.8wQ6vves7nGd-Xfmc3DjVHiebVSH66MN +1941 NC_000003.11:g.10191510G>C genomic False ga4gh:VA.IS6S1FE7xadq7V6aZQNerhZrSDfz6RwF +3557 PTEN S170R protein False ga4gh:VA.btHJ2KuomCUcxWa4p4OuE_Dw2zQ_PBEH +1784 NC_000003.11:g.10191555C>A genomic True ga4gh:VA.B90cLa2qEBWt80H92js_5r1xHlQlDmnP +3391 TP53 S183L protein False ga4gh:VA.1GUcDvUoo3DbirQU0f6C1gEhNgyXWDcd +2161 NC_000003.11:g.10191555C>T genomic False ga4gh:VA.h5LlTYjOogSGp5j44I00bLkTko0MKyRl +2503 NC_000003.11:g.10191555C>G genomic False ga4gh:VA.X17-Rmml_L0QrlUDMPqnUWKR_WQODHk0 +2100 NC_000003.11:g.10191555del genomic False ga4gh:VA.2YCA5U89gtIHq-c1DIDzK7etJoez9wjh +4393 BRCA1 S1841N protein False ga4gh:VA.ZzQRGEvRvGc3Ny8C1zfm1oBeVP3i3Weu +4394 BRCA1 S1841R protein False ga4gh:VA.HSow0Z9f_bCJlIo2Mzu92iNX45kqjNlj +2347 IL7R S185C protein False ga4gh:VA.gz_WX-u1TgtcJp6z-yu8gbFtjUIDmRPD +1671 ROS1 S1986F protein False ga4gh:VA.sRzXsqqo4Mg3KrdKNmdOKPtee1jroyor +1670 ROS1 S1986Y protein False ga4gh:VA.PTul_XzQqapOsgahpYSRMTdXzFnAt152 +4290 MPL S204P protein False ga4gh:VA.b_yUqT_pJxxeJhwKXqZUr0AwT_vb3S5v +10 ARAF S214C protein True ga4gh:VA.thaNPIsobhJxAwkWJ_0BALvT2XyOo6mj +4410 ARAF S214F protein True ga4gh:VA.idgxhZ-14Pp-fAGzTtduSpYGfKo8-vop +2715 MTOR S2215F protein False ga4gh:VA.Aq8eXBjeZRujcpW1Raoo7KQk4NC-klWK +542 MTOR S2215Y protein True ga4gh:VA.1YCBQdNjYjlWFLodUB1DSpykv1YfxTp7 +4472 ARAF S225V protein False ga4gh:VA.zaJuMVy7JmAz-FmuC9TK-15Ff-Y6A7Tx +4143 TP53 S227C protein False ga4gh:VA.p8MiHaJHzAFehP-Y-id5S_ZKKmgS11bZ +243 ATM S2289* protein True ga4gh:VA.9404wyzLJYdacMRPTyyx8b6As8kuy0F2 +1065 TP53 S241C protein False ga4gh:VA.Yr2ywgo8vMyAj8MUtGqTEd2RdiuCdNhD +2777 TP53 S241F protein True ga4gh:VA.BqCnkASMEK3MANfrbgsCBOsh-RzirwqX +3788 TP53 S241T protein True ga4gh:VA.jjt2BiqeJh1wQQ7hpOhc14TM8XI-37Lm +628 FGFR3 S249C protein True ga4gh:VA.g3wMkTfExru4z6L-cpP5OgujLJyvQQfV +4312 SMAD2 S276L protein True ga4gh:VA.mc0LnDRIA0KP0PJzi4p6mFmeIcks5f_Z +1562 SMO S278I protein False ga4gh:VA.sLcwxIca3ovbpaMBYKUiWTxzYDnqxOLw +2946 FGFR2 S320C protein False ga4gh:VA.tOHG7x6MGLpicSKOmXm3LBubm5TQ78E7 +3710 AR S334P protein False ga4gh:VA.k1HEJxD-HaRUd78sj4cMprPvKvsuRU2- +3254 CTNNB1 S33F protein False ga4gh:VA.KqqSau72C5Vm7fSUR3MZtMm1y_jURTKt +2281 CTNNB1 S37C protein False ga4gh:VA.RvX037LrDSf7Psa-l637ibwVt2zvxcZS +3135 3-10183643-T-C genomic False ga4gh:VA.IvAYR8X7uO6a3ilCouAyCfqFIn8Z9Jhx +1495 ABL1 S438C protein False ga4gh:VA.CI6Tn17WupCtJjV5I5Bm3J21s67ZuIWe +2615 EGFR S442I protein False ga4gh:VA.ZYV7Ae4e9hHp3Q3bd-Nx_wq1krqowcFW +2614 EGFR S442R protein False ga4gh:VA.yf8HEvxHsLIQmiNWA5VRDZdexTJCbeMj +2897 NT5C2 S445F protein True ga4gh:VA.r1Mlxlg-Rx1pIyPifalDIaRApq2eShY6 +3502 ERCC2 S44L protein False ga4gh:VA.DXRcu6aDgI3UbEys8q0RcpSZgOsKYDAF +1832 POLE S459F protein True ga4gh:VA.AO9wJcokxJhYb2uAdi5QvWHwFBD0kaHf +1286 CTNNB1 S45F protein True ga4gh:VA.IkwTQj1wXZ1ZvmC0q4T-DHFzias1Z7BF +1287 CTNNB1 S45P protein True ga4gh:VA.hKYqEJaVU5QPbwvTY31a92skDgCHT5Td +692 ESR1 S463P protein True ga4gh:VA.--gbX1Rc0uJuPjDfrrc-n8UopxHSbfVh +2601 EGFR S464L protein False ga4gh:VA.jSiBnokoo-qWGQKGlEd5DdMFEw3GXjLv +2602 EGFR S464T protein False ga4gh:VA.EgnzXQLdRPJ8lLT42xj7b8zI0ALIFgO_ +825 ARAF S490T protein True ga4gh:VA.1mflpNdJ-Yt1Z9XQpeqmlueiPnEO1Dk7 +2610 EGFR S492C protein False ga4gh:VA.-KdOvpCV42-UWbFiJNnQfDhBInw8i8lL +453 EGFR S492R protein True ga4gh:VA.z2MNERgHuX0CHxzxgwWYyHOtmURPMoy2 +1206 KIT S501_A502INSAY protein False ga4gh:VA.RZ7vXRxS_p0CkEOgnlBIUC5Zj8G5bmBm +1589 SMO S533N protein False ga4gh:VA.Piw4wsGUDKtS9RE9m_vDCA3rpMJukr6k +1290 JAK3 S61C protein False ga4gh:VA.hZOtCRHhaobhRaqPC7VUXamyrerI_cx7 +1659 KIT S628N protein True ga4gh:VA.AySXvsmHMBGzVyAqVanO6NI9v2l3hv8e +4408 EGFR S645C protein True ga4gh:VA.1T80e-QuecOa3p1I3-BHtm8hxFbsTTgg +2956 JAK1 S646F protein False ga4gh:VA.oOVv2HFMTSUocYkFIwdDz7ZPjMzv0a-3 +1811 NC_000003.11:g.10183725C>A genomic True ga4gh:VA.tyJNLyJ_KQNWcvW9x-WIZqyxYdRESTht +2011 NC_000003.11:g.10183724T>G genomic True ga4gh:VA.s5F_7fMj-_wZYfXjJC8MDierHw4OAc8s +2130 NC_000003.11:g.10183725delC genomic True ga4gh:VA.IAwucjZ_HISUTZWsaM4OXoP-SuSgUYim +1788 NC_000003.11:g.10183725C>T genomic True ga4gh:VA.Udu_BrE7bGIiQVXpaXhgwuU7xAK9ayxU +1903 NC_000003.11:g.10183724T>C genomic True ga4gh:VA.-2WGhEZt9E5ZRdCasVBxOdGTKvYQvnT7 +3048 NC_000003.11:g.10183724T>A genomic False ga4gh:VA.oMLu78YpYgLJ80n5bWYeUwl0Sr6GyKuF +1787 NC_000003.11:g.10183725C>G genomic True ga4gh:VA.PqhkAHKCVDkUISuqOKhWrmTxthW6Oxsk +2122 NC_000003.11:g.10183734C>A genomic False ga4gh:VA.qDZJowp7Ofuw41n-bOj-QC19meNqDMnZ +1873 NC_000003.11:g.10183733T>C genomic True ga4gh:VA.9K-G1vGCEO_e_KYV_N6Z7lzNnXqqd9eP +2012 NC_000003.11:g.10183734C>G genomic True ga4gh:VA.jwa-BRecFShyVNn44Snoy0BBBMW4zgtt +980 KIT S692L protein False ga4gh:VA.jMzB7fS5fBq3ey_5gLlvLVlxRFl7bisq +822 JAK1 S703I protein True ga4gh:VA.VqfH6LlZhiPpnZ6Ludgq7onGLVQthsQb +3680 JAK1 S729C protein False ga4gh:VA.ooOgI6q6qKh0QH2YniXmhLwbF4dENUlR +1904 NC_000003.11:g.10183745T>C genomic True ga4gh:VA.WQi6tNus7V_R6v_hQgLVAdx_s5oqj0FQ +1816 NC_000003.12:g.10142061del genomic True ga4gh:VA.6OR4OL46XxKiGkt5q7DpVJRiDSuGDHxR +891 EGFR S752_I759delSPKANKEI protein False ga4gh:VA.47Vq6DKst3vqMAfZRKLC1qF1r4pIgMUY +562 EGFR S768I protein True ga4gh:VA.LWa9Hb46vz9hNo9MQ5EAgXyNyAPDmtJu +1443 EGFR S768N protein False ga4gh:VA.UjK73yiz2yRzZjVK4QU0BjrEI0VFH01K +145 DDR2 S768R protein True ga4gh:VA.0cukn-wGPewE0zNQl_sD8xnfIw5pih7k +1182 EGFR S784F protein False ga4gh:VA.paDt0d6bazpi-ifY8_8iIqsPkXzy15Uy +2106 NC_000003.11:g.10183769A>G genomic False ga4gh:VA.MtfZNUV_TTGEWojnbKDOdkug6k324582 +1757 NC_000003.11:g.10183770G>T genomic True ga4gh:VA.72cjKzNZ5ZnHqvOixKhNLRV-guWGB9K5 +2701 CBL S80N protein False ga4gh:VA.1QGctWqgqirgPE1tFrNI4Is2KOtZ7o7w +1874 NC_000003.11:g.10183770G>A genomic True ga4gh:VA.94CDtHuVb4GgE20juQWcqJIk20jlxb3L +3347 SPOP S80R protein False ga4gh:VA.rguHSj3ZuPlcFgcrHUSNQNQSSTe3MRra +1963 NC_000003.11:g.10183769A>C genomic True ga4gh:VA.F9UcyNvxW4oJ8bMmKDjDBal8a46zuRcC +1792 3-10183771-T-G genomic True ga4gh:VA.DyZUwqjMGj0D1TpLha5iLTWYLfkVj_hG +2512 NC_000003.11:g.10183770_10183776del genomic False ga4gh:VA.tP60dsRun36cNH7mrcFd924GEaPY-pR1 +2511 NC_000003.11:g.10183770del genomic True ga4gh:VA.CPUk8aZ3mKvgSDCriCBDVf060t09ObyW +3750 ARHGAP35 S866F protein False ga4gh:VA.8CX-5LKl31wYE-Nz0mzbt0vSO6nX5Rya +262 ABCB1 S893T protein True ga4gh:VA.LmsP0CswXoLGHfLohxxMxAVXWm43Fx2L +3652 KDR S925F protein False ga4gh:VA.x1P7TvR_pmKMFNf6aWfKHU4QpHuOab0s +3645 PIM1 S97N protein True ga4gh:VA.tiHsLvOsmE_1U8vpJ-zUDVuzs8H74swm +2534 NC_000003.11:g.10183874_10183881delinsCG genomic False ga4gh:VA.JxA0G-pjIki2nYS2gTGxsqQPoM9cxQYl +2104 NC_000003.11:g.10183876G>C genomic True ga4gh:VA.yaf2D5EcDWqGl3l_c1pihMulc89Rzr8i +2461 NC_000003.11:g.10188323A>C genomic False ga4gh:VA.mdlfvRXCuIheDvqxwR9OrppQOqAhPrDJ +2065 NC_000003.12:g.10146639A>G genomic False ga4gh:VA.0NYigUBN3E3DviCPJx-JgvYHcyVsRvfG +2146 NC_000003.11:g.10188323A>T genomic False ga4gh:VA.bfCM2M2xfdZ5eVSmlZEKOGORgtcRzCV1 +2292 NC_000003.11:g.10188328C>T genomic True ga4gh:VA.lH08C73QZ5L_CB0cHl6mLxGxEs0kLXqG +1681 NC_000009.11:g.5070054T>G genomic True ga4gh:VA.dkg38nnlZF1SijnpYe4erRvCNFasm6rY +4374 NC_000007.14:g.116771990G>T genomic False ga4gh:VA.SBWNHEBsNB_phrbVZeJVowd6ciNplS-3 +4386 NC_000007.14:g.116771989G>A genomic True ga4gh:VA._QnF6RzFa2X_99EhA7BVCKVGFmGo4Btv +2114 NC_000003.11:g.10183872G>A genomic True ga4gh:VA.KZ6ahrVC0R8xVGkGyKoOC72-7ndHyP9t +2074 NC_000003.11:g.10183872G>T genomic False ga4gh:VA.FH0CjHOyN_uXFgy4Ai0Q21KCcbnTLnSU +2017 NC_000003.12:g.10146513G>A genomic False ga4gh:VA.qfFCME6kN9evuhaYpIZCCNd_jfayfzVF +2454 NC_000003.12:g.10146513G>T genomic False ga4gh:VA.41_QjoNlwVjhJeaQboKxy-tcjrp5csCs +2133 NC_000003.11:g.10188196A>C genomic True ga4gh:VA.AY7ki6x-7kujLEFRuxBndazY4kTLxobc +2504 NC_000003.11:g.10188196A>G genomic False ga4gh:VA.BSj7GQLTpWyP05w47NMg9h7-CM6WJM0a +1972 NC_000003.11:g.10188321G>A genomic False ga4gh:VA.2M1lnvtYDU6wZUvA3fOb_RA6LHtOBmX4 +1998 NC_000003.11:g.10188321G>C genomic True ga4gh:VA.Lu_mmo31qjvPPFet3n8fPNj7YUt0eo8m +2048 NC_000003.11:g.10188321G>T genomic False ga4gh:VA.az2dsQWa9Tg0wi8q11zfu1rO0m7e0g-N +2075 NC_000003.11:g.10188322T>C genomic True ga4gh:VA.l0trIViwkwvWOzdMErCgxpThCsOo82DM +1974 NC_000003.11:g.10191470G>A genomic True ga4gh:VA.ZIr2QaQA1YDdymFoio1XhaDIL4U5mVnx +2077 NC_000003.11:g.10191470G>C genomic True ga4gh:VA.7h7y1e4KacaKIWKcsoEI_X1UcSb-JEXE +1990 NC_000003.11:g.10191470G>T genomic True ga4gh:VA.pzw-jGDX_K8TS2jydT5YL7pBjg6SV6oW +2093 NC_000003.11:g.10191469A>C genomic False ga4gh:VA.bfRqPva5adP1azA793GfLPwzvJ6zjhpC +2078 NC_000003.11:g.10191469A>G genomic True ga4gh:VA.YneVIYMADlEffL-oD_Q15vax9CFR9XcX +1992 NC_000003.11:g.10191469A>T genomic True ga4gh:VA.bY-XOw7978Bpabmy2_ANcy7SvIJHBIWL +2248 NC_000003.11:g.10183829A>G genomic False ga4gh:VA.vWCOWDpDFR1dTzTy9Vl_opz4WaTACWRo +1839 NC_000003.11:g.10183844A>C genomic True ga4gh:VA.Kg3pCMI94uaWYHFC_VODMRZRK0ITdFUj +4330 ALK T1151K protein False ga4gh:VA.VVF3Hnr7bX4WgjmugbvqTTzxxgBSct2l +1493 ALK T1151M protein False ga4gh:VA.4NjTL4i6_scVuPoZR9Tdq4_zGeDTqkI9 +743 MLH1 T117M protein True ga4gh:VA.HWS5pHXZGKqS4vxlh4-hAnMu-CaVJNZ1 +2054 NC_000003.11:g.10188228C>T genomic False ga4gh:VA.Yj2Ueq3RlboieittW6oYimDNy13VTbR5 +1905 NC_000003.11:g.10188226del genomic False ga4gh:VA.Jfnx6OF0ScnMkkQu6X3nJopS7n_dScRf +3417 TP53 T125R protein False ga4gh:VA.UYscgwwiJc8XAGkYtXclZ0piqqqbZ0cP +3684 TP53 T125T protein True ga4gh:VA.Avfw6gvO4pliSVdewxBR7EIucPuY8N1b +1843 NC_000003.11:g.10188254del genomic True ga4gh:VA.gbTEIIlsKnJNHcuwfHOfhKOTd1oZkeca +2085 NC_000003.11:g.10188312C>T genomic False ga4gh:VA.gp5co_9CoxVoULGnkRG8ocn10gRU8AJn +3130 NC_000003.11:g.10188311A>C genomic False ga4gh:VA._PRjxBqr9Q4-6wYi03EbhB65pXO77t9a +1745 NC_000003.11:g.10191477C>T genomic True ga4gh:VA.n1DjZeO5KcnvdcbKmsRO25qyxhso-_Df +2323 NC_000003.11:g.10191476delA genomic False ga4gh:VA.sDA8K3qL_xC-XtinZ84gKRgqQZp_JpAP +3558 PTEN T160I protein False ga4gh:VA.tXh7w6MTvRtPe1RDE6sYYPqvfhZZXvbW +4398 BRCA1 T1700A protein False ga4gh:VA.wJ1ex3b9pvDOZI2ukJuykW6EC7z3R7kN +3979 BRCA1 T1720A protein False ga4gh:VA.SOkKg9JfJTIxSnSWZJ4J1ndK2zQxtcyY +2712 MTOR T1977K protein False ga4gh:VA.Ji9aw4x9WsoZHeA20McQ6P80U3lNqr7N +3412 MTOR T1977R protein False ga4gh:VA.JMKQlllh0Sb_0umnMgDPWpUXiv_GgTyU +540 FLT3 T227M protein True ga4gh:VA.C-ArSx622Lnc8UXYjtznX91-yZQ7sukX +3782 TP53 T230S protein True ga4gh:VA.49Kf_Q1N4T772ACSaSNGpoWAWOsXjqaE +1587 SMO T241M protein False ga4gh:VA.xyiJbsUaa-wnFNSGMK2H_84iquKfr-d0 +995 EGFR T263P protein True ga4gh:VA.iiK8HZSJYJF78er_o0Bd38U5JM43fJ3w +901 ATM T2666A protein True ga4gh:VA.Upz-TjMnQAi86nzX7zWumAHmaFNcvJgu +3629 BRCA2 T2722R protein False ga4gh:VA.m_VR1gveM4LD5wua-mTpPbbVob4Yncd_ +3407 PTEN T277A protein False ga4gh:VA.bfb82eAmKL-T3dQliQdZ58HSFafCFxox +3406 PTEN T277I protein False ga4gh:VA.3sIXby2dGUIWUEjdnQtUhaJQMbEBG9y1 +3403 PTEN T277R protein False ga4gh:VA.VQys0bPjzxErl5wCKGLG2zNt82R8d0CJ +2918 PRPS1 T303S protein True ga4gh:VA.YgI5ylY0uQkhORyhBQmbBKPbzGTKGQox +2 ABL1 T315I protein True ga4gh:VA.M3CbaYfwomLqvJbdK4w-W7V-zw7LdjGj +870 BTK T316A protein True ga4gh:VA.pDs27WIFyfAAvovhA7i3Afa8sYkpzhY0 +2618 EGFR T415M protein False ga4gh:VA.xJZOw6s1YsZjkcUEA7sRm8sTPkkoeOTD +2620 KIT T417_D419delinsY protein True ga4gh:VA.kM6ncx_QVeRAHSczwTq6G1psqn2Kzvlh +1285 CTNNB1 T41A protein True ga4gh:VA.B4F4h08PbEFiDd28WS5PASxkvla4gZQj +3503 ERCC2 T46S protein False ga4gh:VA.DYWIkbv7EBioOW_ka5iZZJZeJEmT7GWy +2795 BRAF T488_P492del protein False ga4gh:VA.wf13enk2gAOHMV1TOfg4NaUEZNwH1zjf +974 KIT T574A protein False ga4gh:VA.3pibdPDBvXoi9Lxylg7rjDkD8Sx07gE9 +2824 BRAF T599_V600insT protein False ga4gh:VA.e1ZU94S5TUpcY98Y6YBsxuJHZ1v0PYj3 +2387 CSF3R T618I protein True ga4gh:VA.drA4rCaD32eIv9v7YzX0VsfO1svIWD9L +979 KIT T661I protein False ga4gh:VA.FZm-zbDdcVOXO2B70ingKQv2feMF2bb7 +1267 KIT T670I protein True ga4gh:VA._L7r4YO_nW3etQySFzjREsHI4j4qnzPv +861 EGFR T725M protein False ga4gh:VA.2qZUU5_hFkU_92Q95pqnwo6aA4QAupIT +3686 PTPRD T781A protein False ga4gh:VA.pmhg8R8tYbK8GO_q5DQmEKe1k9V9ISUF +1573 EGFR T785A protein True ga4gh:VA.NVSHCSq6FSiwJe5EkTn2vyFzK7YiEG5t +34 EGFR T790M protein True ga4gh:VA.BldHTcxmxpKf1exsSbeuki1jhdek1GaJ +2331 ERBB2 T798I protein True ga4gh:VA.XS45OyjwZDw80epMsRThKa__Ruiesm5b +1305 ERBB2 T798M protein False ga4gh:VA.smZxiaSKdJlI3qDxctc5uzgWTynxPNYA +4321 NFE2L2 T80K protein False ga4gh:VA.2LsgZwSGI8BmXZSMKw54CjsGbFBvRCZb +1463 EGFR T847I protein True ga4gh:VA.PyXUrAIAvFuTCqthgeRxymir3RIF37nC +1467 EGFR T854A protein False ga4gh:VA.gvzV1FM8fJ6_IAOaZ7cx297dIjAlppsi +871 ERBB2 T862A protein True ga4gh:VA.KIkgyRZPv7aOgAhk3AYUlDJzkWJWVsU9 +701 ERBB3 V104M protein True ga4gh:VA.7eE-LW97KWY5OoTmRZ0CQXGI_gRR9ri6 +528 ALK V1180L protein True ga4gh:VA.Lu9Sqdtq6vK3nmoMiOjtLJVt8-TPkRmV +1875 NC_000003.11:g.10188245G>T genomic False ga4gh:VA.l063UrDhlBBR0fcjoRA7YwZUqcGgW4TL +2380 NC_000003.11:g.10188245G>A genomic False ga4gh:VA.oUrtg6CGq8HQFCQPsvjQvsuiK77z3JsB +1970 NC_000003.11:g.10188245G>C genomic True ga4gh:VA.z3J9F62UAS0T66raT7mjYoYd2ycg2S_c +1254 TP53 V143A protein False ga4gh:VA.essrZ9LQVugaAAtYK3wwNEA1vnUFNVGV +4411 ARAF V145L protein True ga4gh:VA.Tb5JbCLdIgd-xvJ7Z7qisV4AHdYeCTaO +2991 KRAS V14I protein False ga4gh:VA.GrJfhOcKR83AxB64jebuRV-Dt1MrW19H +3968 BRCA1 V1534M protein False ga4gh:VA._AV2Bz5mDsY84g3FQUPF36KOdujSjWdI +2836 MAP2K1 V154I protein False ga4gh:VA.trOVEEcLhRExB693nMB0wEmpUFCxH4I- +1909 NC_000003.11:g.10191471T>A genomic True ga4gh:VA.S1kpMfHOkheGPXPwABDj2mnMKBpFalqp +1934 NC_000003.11:g.10191471T>G genomic True ga4gh:VA.QOKq-VFwIcJ0gno65-sanJcsm8PlsMlJ +2076 NC_000003.11:g.10188320G>A genomic False ga4gh:VA.eyY_mtRSC6pAHnJD9alrfaw61rqZjjYp +3059 BCL2 V156D protein False ga4gh:VA.RqNW2OUpWqp8wxOOSciWi8ZRAvVCDqtw +1143 NOTCH1 V1577A protein False ga4gh:VA.CpdL4LS-DiODGiHMn0U7SuXCT5Yy4doB +1144 NOTCH1 V1577E protein False ga4gh:VA.-PJW4BKv_QLz9C0zcR9Gw2gqIr9lqQxx +3574 TP53 V157D protein False ga4gh:VA.xN71-ANTvo1ofkgpfa_s5vNVW0yVC9bu +1092 TP53 V157F protein True ga4gh:VA.zjPelkCq-mrQdo1OsslmXcJFhJgNTzWO +1249 BRCA2 V159M protein True ga4gh:VA.mGC3zkPtoj_gLRt68FxA3BC0RLDpJbwz +2437 NC_000003.11:g.10191504T>C genomic True ga4gh:VA.bCw3OTfdnwPlavNOI74rL7IUwfxTFlNH +1775 NC_000003.11:g.10191504T>A genomic True ga4gh:VA.GevAJlxcHhbUFyXyxL4ZNUmfIAViK5bs +1825 NC_000003.11:g.10191503G>T genomic True ga4gh:VA.t4b1zez9cgxmK44dv53IRwcfQyuaSyD- +3554 PTEN V166I protein False ga4gh:VA.pjJgOLC2JKb1B_q067OaH6ZENG_CVi5- +3970 BRCA1 V1688del protein False ga4gh:VA.kDvA69XltzgjFaAjL3ZggwfUtpGpM77Q +1910 NC_000003.11:g.10191516T>C genomic False ga4gh:VA.FqG4G6stfIyTo0eXoMUJMXy27t2iH3Pn +1826 NC_000003.11:g.10191516T>A genomic True ga4gh:VA.4A3W3yBqr22lWwp4vLZhVJKcPRiYwXbe +1806 NC_000003.11:g.10191515G>T genomic True ga4gh:VA.9kVDuVBNV35Sl1jHmrIRa0OJEeoIu3AS +1935 NC_000003.11:g.10191516T>G genomic True ga4gh:VA.Y27UYD9f75EDHZtmbeVoWPzbAYdq5PXp +4399 BRCA1 V1713A protein False ga4gh:VA.mCoWigeAPENAk-JEV0My_QaWqctLhzwk +4117 TP53 V173G protein False ga4gh:VA.WHRFPQ8c1FT-2YKgSV9bqDQv0zfNtUtW +1086 TP53 V173L protein False ga4gh:VA.lElcv6zHvpCbNPBjRYSFV2Y0CdR1uJXH +4139 TP53 V173M protein False ga4gh:VA.NGaIOGOnIvw2ayW4vwFexYAM3TZG0XbC +3998 BRCA1 V1804D protein False ga4gh:VA.Q8kWciM9HCQUo2RBEec4aHSP6hZ-mYHF +1847 NC_000003.11:g.10191547_10191550del genomic True ga4gh:VA.x05D5l5Je9fOWT2RIoxV8xvl5akWCtWh +4396 BRCA1 V1838E protein False ga4gh:VA.Oh4LOMlQb5ivgdJVXUWEWRDdBB-cWkNT +2493 NC_000003.11:g.10191588T>G genomic False ga4gh:VA.Yz3C2-cTGz_4Y-gVRte9XpTBnHg02Gt1 +3595 TP53 V197E protein False ga4gh:VA.jcHpcvTpxg8kXF6RAh1pJ2X_XSYO783X +4120 TP53 V197L protein False ga4gh:VA.1TVGOWkQy_2FJaCilqadeG9p3NiulzHl +2805 MAP2K1 V211D protein False ga4gh:VA.RciqSdUxkCx924gJYBgnJpGTI58nQY-F +1251 BRCA2 V211I protein True ga4gh:VA.4jkE4N5enTk2FlQYQQqpJvxS1WykESod +1250 BRCA2 V211L protein True ga4gh:VA.0qH7yKSrFqa-5ygYZ91lnSRKWIbrkQcN +3507 ERCC2 V242F protein False ga4gh:VA.CshJQHpS_jY4a4i-9KQuUuTUKj94_tiP +2348 IL7R V253G protein False ga4gh:VA.nwL0x43kC2j4BF28cXOyZtNSgX0JYyIu +792 PTPRD V253I protein True ga4gh:VA.UcQCcRWDQIvy8ElyFtDJOf7rxkSLIpgp +4123 TP53 V272G protein True ga4gh:VA.XdKdUWIZCeh2-tKSDh0Hg6WPGE2X6a-e +1035 TP53 V272L protein False ga4gh:VA.17uK9mF0eh7-jBBG-LnqhjnO1cF0Wbz2 +3790 TP53 V274F protein True ga4gh:VA.Q3YKPFaFzlw7l3mKDOBgx5oyqtJhkGfy +2751 TP53 V274S protein False ga4gh:VA.qbJjBDilsNn6tFlMErMvshYzJGsl-fHe +1604 ABL1 V289I protein False ga4gh:VA.xfuFhQfN-kE-z4szAZ6xYHN0UxzY786j +2277 CRLF2 V2del protein False ga4gh:VA.je-LVhT14HXZ49lznpjTHUReUTQ8oQ-m +1576 SMO V321M protein False ga4gh:VA.fhYNohKpNTUFO8MkC_5ypxX90aaVfElG +775 MSH6 V352I protein True ga4gh:VA.UJ6RM2f-PblQ6BYS2zZIQkVjdpSHOmQI +2841 MAP2K2 V35M protein False ga4gh:VA.XqiT1RejtUDafaZtfvefnNI0a-_wcDmJ +2702 CBL V391I protein False ga4gh:VA.HwmYlN3zK2dsbEzYjnEHPOw-Zds1cmhV +1831 POLE V411L protein True ga4gh:VA.yjap3q4PDDNQz0e8gX7pOCPrVtGzeU9r +2612 EGFR V441D protein False ga4gh:VA.4s6Zn-f2aEJiIHjmprO5P3TUqX7iSn2B +2613 EGFR V441F protein True ga4gh:VA.w4r6Wp3BuWKRZz8qs4t5E_XU-MPQG9Ba +2611 EGFR V441G protein False ga4gh:VA.pC2nPd_TojaRQOjTpSelfyXPNPga-ADp +745 MLH1 V49A protein True ga4gh:VA.qGPDk6t8lfXNkMeqaTm-u8q72Vjpwo42 +728 MLH1 V534R protein True ga4gh:VA.vtBAJQkymh3oJGPNlrMwOc8-a9tzUGjm +2938 PRPS1 V53A protein True ga4gh:VA.35O5EKQylsLGlU_r6v7MrGjglhVXwQFv +3217 FGFR4 V550E protein False ga4gh:VA.OpO23Al8eybCG_fxdKKczSVSkD3TBqi0 +2399 FGFR3 V555L protein False ga4gh:VA.iUWKWRqtvfzv2Mks8b63PPmvlu2P5XKV +2400 FGFR3 V555M protein True ga4gh:VA.3Ww6mJEaz8x1hHp4AYhkKSyXUnQtAamu +1543 KIT V555_I571DEL protein False ga4gh:VA.IPGvFhI5JPQ_EgvprHHjzN2hgFQRQ0wv +957 KIT V555_P573DEL protein False ga4gh:VA.bQ1afDXed977PesvRFj73YYpWR9pkPEQ +956 KIT V555_Q556DEL protein False ga4gh:VA.1DA36cCD94HrFv-pcXD-WlQIZF7sXAaa +2695 KIT V555_V559DEL protein True ga4gh:VA.7gEcqCNANmSaRdoyxTx58dXHvIr8mLOy +969 KIT V559A protein False ga4gh:VA.nPBn1g_GPr7nSNOcDBor9pLGJsyZZZoX +968 KIT V559D protein True ga4gh:VA.9_q4YYFXHMgrXll20pwJJTH96bJkVfRp +966 KIT V559DEL protein False ga4gh:VA.MrQAtOTEAvu5UTpm3GJ7nV3NbZiBhS3F +970 KIT V559G protein False ga4gh:VA.rdmWjmfv5r1vV2x97NdpqzKodyj5DMPp +967 KIT V559_V560DEL protein False ga4gh:VA.-KZMu4Df1DtLjej_qbYqU6T-o8pGFb8f +971 KIT V560D protein True ga4gh:VA.mJyvi68_kx2tyhXEqoU2UAcockZUkgUl +202 KIT V560DEL protein True ga4gh:VA.MrQAtOTEAvu5UTpm3GJ7nV3NbZiBhS3F +972 KIT V560G protein True ga4gh:VA.pAcv9K9YrZo6SFWjTnOAqiTaUoz43sjB +1550 KIT V560_L576DEL protein True ga4gh:VA.kFypumQf7CgTQDq-b-4KBxa8gQfXLWhT +247 PDGFRA V561A protein True ga4gh:VA.Pz0u748g3gbhMfO0A3gUsMy0y1XHOckA +941 PDGFRA V561D protein True ga4gh:VA.0qqy0dI_wNO9Gc4B08RYh7tKvdBDA_9l +2781 FGFR1 V561M protein False ga4gh:VA.Xhk6XFZEAZpgP3WLGdNPoc3wz1okOEED +1551 KIT V569_L576DEL protein False ga4gh:VA.NmINkxuCD1yGiyoJIzqEVg7s67D_uZzx +1632 FLT3 V592_D593INSDFREY protein False ga4gh:VA.WX4OadEDC_x1AVsL5kgN_pu3L-PUl2Bf +11 BRAF V600D protein True ga4gh:VA.-jYzNKdhjeSB-H_yuZobCWD-jqmUkFVl +3452 BRAF V600D protein False ga4gh:VA.-jYzNKdhjeSB-H_yuZobCWD-jqmUkFVl +12 BRAF V600E protein True ga4gh:VA.ZDdoQdURgO2Daj2NxLj4pcDnjiiAsfbO +1199 BRAF V600G protein False ga4gh:VA.JT7maodV4XKLl4W-t-WFLEIvJ8jWmPCl +563 BRAF V600K protein True ga4gh:VA.EReJZvr-VBO8123VDpv4Gvg0jvLZh_gH +1404 BRAF V600L protein False ga4gh:VA.Ktev5asCsmUbHaQG6N-CdSp_g5FyJxLN +1405 BRAF V600M protein True ga4gh:VA.c3Lavewm1iqBcY94C9KyS00Tjh8pJ5um +16 BRAF V600R protein False ga4gh:VA.MVkdENtL2ZtH9srzcbGGI7mRvxG5DkVW +991 BRAF V600R protein False ga4gh:VA.MVkdENtL2ZtH9srzcbGGI7mRvxG5DkVW +1658 BRAF V600_K601DELINSD protein False ga4gh:VA.TD3QgWuH-369DIAkvRESW7AQKg3fG-Ij +3241 BRAF V600_S605delinsDV protein False ga4gh:VA.5lZmJisF7BOh0yL2l1ZO5BmW1An_IwQ5 +2834 MAP2K1 V60E protein False ga4gh:VA.wYB1cptUfaNv3XLKCagYXLB3PHBkFLHm +64 JAK2 V617F protein True ga4gh:VA.JiaDMZmDvTa7T_zVcVX8UWf4x9X6jG3_ +73 KIT V654A protein True ga4gh:VA.2jbEOWQLfQD0H3qVUZbVKlzA1EBhvA41 +3205 PDGFRA V658A protein False ga4gh:VA.afy9jLeTCluCri009-kOtO_F1kY-wLkw +1789 NC_000003.11:g.10183727delG genomic False ga4gh:VA.QZJOk5GHlrHxhwqaACqMjMMx8RZDIhUL +1936 NC_000003.11:g.10183728T>G genomic False ga4gh:VA.n0jsO06zdZtTsN6BsOZoKngDhclph3pk +1289 JAK3 V722I protein False ga4gh:VA.nrmPc0xPcl0tIJmJBRB2ZBV2FrJzTq7e +3230 RET V738A protein False ga4gh:VA.PKwVBSTaJ701dVyyZmkDJBGET1bCHHlm +1001 EGFR V742A protein True ga4gh:VA.lAsK40rgloDF4sA02EGIC_Qw24j0A2Tx +1999 NC_000003.11:g.10183752T>G genomic True ga4gh:VA.2tgoGc4zD7NjkwOagKRQK0at4JX59w0l +2270 NG_008212.3:g.5426_5445del genomic False ga4gh:VA.N0MGPT_1x9MVICMIOzDkoJDJNR_b-Hv5 +1578 EGFR V769A protein False ga4gh:VA.1TSyjZ9dzPXecFI5bDTeXomMbANuzuJn +736 EGFR V769_D770insASV protein True ga4gh:VA.sHKHDIuSUmV08aL2O-J3T9KpVc2-9SXN +872 ERBB2 V773A protein True ga4gh:VA.v9yEuOWvlQwq1D-BkMh3GImIldePEtgG +1311 ERBB2 V773L protein False ga4gh:VA.ES7VOFhPywNQ2xuAmX7r6U_OhxYqKyu9 +1892 EGFR V774A protein True ga4gh:VA.18Sw7VPakYWxrkzxlCtTzIYynx0lXmxS +1894 EGFR V774M protein True ga4gh:VA.oU7gQ3goSs0tI3JKIV8uEYqdx1KUGWOE +1567 EGFR V774_C775insHV protein False ga4gh:VA.bYi5ArRZIpRShuWHoCjAyX0lsjQsvBJL +44 ERBB2 V777L protein True ga4gh:VA.jajfj7FsTfGJKty0CUGISRDu3vfWwMxw +2568 RET V804M protein False ga4gh:VA.i3Wijz4w7QwMom0qmvd-DYEU2WPWDuIP +1897 EGFR V834I protein True ga4gh:VA.ICQ9mDFFUj4Z5RjME0TMfJkwBk6BZjJX +45 ERBB2 V842I protein True ga4gh:VA.nES_ixHiy7LHKPvlNU7m6sx1qg6PyxOr +1937 NC_000003.11:g.10183781G>C genomic False ga4gh:VA.S-elNZU1dzPUlaQSkqsMke0JLMiOvFDk +1815 NC_000003.11:g.10183781G>T genomic True ga4gh:VA.xtTpTTb1Al-vvYerJI-p5WKln5lAOdhK +2101 NC_000003.11:g.10183781G>A genomic True ga4gh:VA.RgDpC2WtxqnX1oXTpL7LvAkf5KpDq2-E +1466 EGFR V851I protein True ga4gh:VA.FCVbhXJSPhcwRRreSnv_F_EUYe2TeX47 +781 ERBB3 V855A protein True ga4gh:VA.wSMWz82udGiK7_SY-dqYa8uQK0umcJuG +2068 NC_000003.11:g.10183791T>C genomic False ga4gh:VA.MDtE149tvD5sUk-GMAZuec7Unpm0dr6e +2513 NC_000003.11:g.10183791T>A genomic False ga4gh:VA.rnuzF16j9T12xO6imTuJ8F2-tydRMuZB +2432 NC_000003.11:g.10183790_10183791insA genomic True 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ga4gh:VA.rNmyo9tkQzvHBuWEEV0fa2y8QhmrgAXx +1555 BRCA1 W1815X protein True ga4gh:VA.kPDhTDJUW7xG7MH1G8Fr626ytZphy_W0 +3995 BRCA1 W1837R protein False ga4gh:VA.rh0DaxT_zelYY8gjw9gaI6W-g841VSZm +3627 BRCA2 W2626C protein False ga4gh:VA.tk9jGt70AIwYBgwgO9hZ8rHHhQOpJXiv +1563 SMO W281C protein False ga4gh:VA.g6LCC1uHUWPI_bTclIrHXHRaKoh5BaqL +1583 SMO W281L protein False ga4gh:VA.WYbxl9NAKnvUMmukzR0M3pPXq4JQFVl8 +2945 FGFR2 W290C protein False ga4gh:VA.6C5XNvr1lx_XmI8AfZskwG-u7GgDgTR7 +4403 CDH1 W409R protein False ga4gh:VA.jIcHUC1yf70ShT0UHhV8-7Z4f_bAyDwt +3688 ABL2 W469C protein False ga4gh:VA.sNNp3pynOa4cYpjV1B20a7cdTAm6k_1Z +2667 MPL W515L protein False ga4gh:VA.ONjwKW5tR0w95SbU5EUCfuPIvQxhWtdN +837 SMO W535L protein False ga4gh:VA.EmwokOFZaZCIOkIcPyF0zwS9Ckw826h- +959 KIT W557G protein False ga4gh:VA.-X5LgVajv8hJeieqJbBFI6PnjHgyUtIH +958 KIT W557R protein False ga4gh:VA.bJNRtqyXrTpZxrFJmZ6yzOhGrDGY-4-S +960 KIT W557T protein False ga4gh:VA.AOWyr032LV6bhT-CHDotpBiVmz1c4_DN +962 KIT 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ga4gh:VA.Xeqe7ACrtlxGJiQkfXWCFkSgkibKEtvI +2039 NC_000003.11:g.10183794_10183796delinsTT genomic True ga4gh:VA.3c2Xik0oUjkcRr4-xwhaw2mxVdjQfvu_ +2242 NC_000003.11:g.10183794G>T genomic False ga4gh:VA.iUATzhYoH-iIO5o5HO_1cxOEyiK58ZWW +1761 NC_000003.11:g.10183793T>A genomic True ga4gh:VA.z3rc6bKCllqpkZDy_6BELb9T9rPnKHPk +2056 NC_000003.11:g.10183793T>C genomic True ga4gh:VA.3gBZO49au6YrUqn3OYgOtSQHFRGMm0ea +1966 NC_000003.11:g.10183794G>C genomic True ga4gh:VA.WzsSnpV4s0SMiFqSiHrde_iz6VCcycQh +2913 MET Y1003H protein False ga4gh:VA.mGlg-1XQozd3aC-hEqn4pYkLZyQvHVoW +935 PIK3CA Y1021C protein False ga4gh:VA.etF8HNjm7urbqzQfnzw-7FuGnaUpghip +1766 NC_000003.11:g.10183867C>A genomic True ga4gh:VA.ZUYHbMpS6WJG2FyaVcyzUGRs0Q3VFkOK +2818 NC_000003.11:g.10183866A>G genomic False ga4gh:VA.B8mNGCYuaxf2FULAPGRl1saEVnZSWUDj +1865 NC_000003.11:g.10183865T>C genomic True ga4gh:VA.3fsteVB2MvsN0kjYiNzcjPLDTG1iFk8j +2006 NC_000003.11:g.10183865T>A genomic False ga4gh:VA.6Q-rS1TplWb3xxpZRcqywZwoWW7q5fCM +3762 TP53 Y126D protein True ga4gh:VA.BeztD_PfRLUkJJyN89jIXPTPu5e7XeOR +3763 TP53 Y126S protein True ga4gh:VA.k-5Mw3EjZUGBRogU9pPk4ZNKDs3NSHbK +3456 EP300 Y1414C protein False ga4gh:VA.havHedEUqE4sCW-9FvXtFtGo1A2FdPC1 +3500 ERCC2 Y14C protein False ga4gh:VA.GjTllNStGCZqrb4oUObse_VX33wNvrw9 +1645 PAPPA2 Y1520X protein False ga4gh:VA._nRs8CZHJO6SOMLT5lu-otysu7p8SQe_ +1968 NC_000003.11:g.10191475T>G genomic True ga4gh:VA.Z_v3OXXE86Aa784GSA1SOIs9fmaiMbXy +1946 NC_000003.11:g.10191474A>G genomic True ga4gh:VA.oUqL666xpKVTZBtEC0PVAGB9DKicOv-m +1967 NC_000003.11:g.10191473T>G genomic True ga4gh:VA.p47WtAKNLli2ZH2mghJovuYWXLpHhvbl +3182 NC_000003.11:g.10191473T>C genomic False ga4gh:VA.MbBUqgYeNd_tKBVGtKOzwBQ8Ml5_oYq_ +2013 NC_000003.11:g.10191473T>A genomic True ga4gh:VA.ZZx4tX92NgFkv0G9qHUDT9RlCp6TKSIs +3193 NC_000003.11:g.10191474A>C genomic False ga4gh:VA.b82uBqPFqMfFElnYa6nkqlC4gNAPrpk3 +2453 NC_000003.11:g.10191472_10191477del genomic False ga4gh:VA.KjPAPjWfPJvJFLvF3WFDWDqmHZcJaXdE 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+3506 ERCC2 Y209C protein False ga4gh:VA.vdvqEkVUm0eGmCVxYmWgXEnd0BjVN_zY +922 TP53 Y220C protein True ga4gh:VA.giksUgnvPGpE_10n6AQzAAg6afUY9tGg +3779 TP53 Y220H protein True ga4gh:VA.G3c4Pyjqj4aaZ-fc8Suv_iC__MdkEWxm +1596 ABL1 Y232S protein False ga4gh:VA.zC8dt1cLcfp7Nl3YkmC-ApQpjM3n4Iuw +1068 TP53 Y234C protein True ga4gh:VA.k6OnmFpvxGkCY2X-Lxg-OkIpWpN8aZWW +3781 TP53 Y234H protein True ga4gh:VA.E346om_SPAP3Vx5od8bThZsMjWHzF54n +3770 TP53 Y236S protein True ga4gh:VA.Yvw7zmfBflXQvP1cyTXVskDC9qykijtb +3501 ERCC2 Y24C protein False ga4gh:VA.tcWp9CHHjirCWvbS5NvJdazzJMURTFix +803 RUNX1 Y260* protein True ga4gh:VA.sToP2iPM8vJzsxy_JIlLvnCcISMo4-2N +3614 BRCA2 Y2660D protein False ga4gh:VA.rRUDp7dsrf1dm-tU-F9RZzZSPmBvBNE4 +3609 BRCA2 Y2726C protein False ga4gh:VA.ThRCnLcQHnvf8bwOwE61qSkUIuImxHUK +3690 PTPRB Y309C protein False ga4gh:VA.L0AgTfqNK2_3_mD7gIRLa5ykKfCEnwLb +2934 PRPS1 Y311C protein False ga4gh:VA.lNfM1kowexITIrWA1ZnekuY2_u-tIbex +3405 PTEN Y336* protein False ga4gh:VA.BFUy3vgUfiY8ratRXIxhHWqLCVT0Snmk +1605 ABL1 Y342H protein False ga4gh:VA.Orj0eWypdYM752SXBeLevo6ROR9IIe_t +2377 RHEB Y35N protein False ga4gh:VA.PfZdoMGnXnApbvZ9Cpia02zlmp5VNXxS +2638 CBL Y371H protein True ga4gh:VA.1Y58ZgJqZI95sgjaJiY1B4JudCUIGBu3 +2404 FGFR3 Y373C protein True ga4gh:VA.Te_5eCSBPCF7A2FyyGRQ5n_86SWBUomZ +3356 FGFR2 Y375C protein False ga4gh:VA.FBfLdzpLardmwPtEPCxJ8Lh2-bkxeJz8 +3065 FGFR2 Y376C protein False ga4gh:VA.FBfLdzpLardmwPtEPCxJ8Lh2-bkxeJz8 +1611 ABL1 Y393C protein False ga4gh:VA.yyfMqqnt-alTogIkCGaRwnM9YHduXwpB +3689 ABL2 Y399C protein False ga4gh:VA.bM61ZsB3_OLw8HTsTFVUKERj83SwmPUS +3239 KIT Y503A protein False ga4gh:VA.15R0nBgTnfGD1oAJYb_JkzMRJ-GKCyeX +946 KIT Y503_F504insAY protein True ga4gh:VA.RZ7vXRxS_p0CkEOgnlBIUC5Zj8G5bmBm +1669 LYN Y508F protein False ga4gh:VA.0ZFVo8rQE2EWbFev-f4qHrl9FEeT_ysA +48 ESR1 Y537C protein True ga4gh:VA.9tHKXDLG33zh_NyyGQkpNsrd_6N3g19W +49 ESR1 Y537N protein True ga4gh:VA.9FkmWqvkF7PPsey-xS60tJpzAz82vbLM +50 ESR1 Y537S protein True ga4gh:VA.ZbIfYAY2biskmygLhun3iV6c1mCraHnD +952 KIT Y553D protein False ga4gh:VA.b0lhbaYds8uRKScYFpAmdsg-XK7wle2c +2737 KIT Y553N protein False ga4gh:VA.WNRBk5ifoKdrwMlQLS24yiH4ACB8lMGY +953 KIT Y553_K558DEL protein False ga4gh:VA.YmmC4ZRP2LVg4L1KmSzISvSz_kTeY523 +1542 KIT Y553_W557DELYEVQW protein False ga4gh:VA.YedXsOc57lO1tDC4lVrijbtYwWs71SeG +1548 KIT Y570_L576DEL protein False ga4gh:VA.FIJkrH6sLf-NMdXBaelRbQQeksdkRE3z +3233 FLT3 Y589D protein False ga4gh:VA.UqmR_XpoxjutyPeicSa7dxpTWtVb13-O +1630 FLT3 Y591_V592INSVDFREYE protein False ga4gh:VA.pOeBFKypSGoGAyinaM4xUOXNgLtgmTru +3607 EZH2 Y646C protein True ga4gh:VA.aAUcrbK61CVCa7O5ZdT7WSds_igHqoEf +2989 EZH2 Y646F protein True ga4gh:VA.fIFZFyzJRiGTt2CRRD2DUSSQ_1cA2dDi +3364 EZH2 Y646H protein True ga4gh:VA.6qph-MXfQbKcjrNnNPVzDR9ZN4esTfz1 +4090 EZH2 Y646N protein True ga4gh:VA.zjbm34xh4ZI54ihvCj8XA-nZQMdSF97I +2666 EZH2 Y646S protein True ga4gh:VA.oVYcvuDJJQ7LB5GP2t-JRiqEKOrsSn56 +3514 FGFR3 Y647C protein False ga4gh:VA.hu3gvJqrEAaVTpH3rpzktTkxjbugx931 +2986 STAT5B Y665F protein False ga4gh:VA.zihvLLhcOI2WqLnI6dGfxTaLkICWcmXx +3499 ERCC2 Y72C protein False ga4gh:VA.cLYTITVebbM7Bkg9Vkh7GAvxnf2b_0L5 +3606 EZH2 Y731D protein False ga4gh:VA.X1zp85G5qQbErS3FDWItT_C9EDFMi3c6 +1665 EGFR Y764_V765insHH protein True ga4gh:VA.o5Eb2v0LXmAVvOvWfUj_YLOqRf8SMlqg +1575 EGFR Y801H protein True ga4gh:VA.DPILQOyn3zBwdByN5YLK6XRtHQXHinVk +3228 RET Y806C protein False ga4gh:VA.yNZC6w5OosG14wQle2aICWojN1R184VV +3229 RET Y806N protein False ga4gh:VA.4Y_gVlftd2Pnufet3yiOeU0TuH8RmPb3 +989 KIT Y823D protein True ga4gh:VA.FnKUBP_GRBWWxX62GTfi19nhU-h0BwuK +3665 ERBB2 Y835F protein False ga4gh:VA.CSMu-dT2HoOt4a2BjZhmuwg3uqYmj0lo +3070 FLT3 Y842C protein True ga4gh:VA.f9-eqHznniEhQ2xMX6700bclESANjHyV +3234 FLT3 Y842H protein False ga4gh:VA.Vf3dHNJ3hDECgeE8xd315gUbl7VY3DrD +3535 PTEN Y88C protein False ga4gh:VA.79VbVuOGMQ2_SVSIFOLK2-Tnw5nSoMIv +1642 POLD1 Y956N protein False ga4gh:VA.Sgqdn3sr69VsP0GpqYWhdyuNPUt6Er3C +3125 NC_000003.11:g.10183825C>G genomic False ga4gh:VA.Aicgzzqle9NaslJ_XYq1VSFTkNzhpOfL +1933 NC_000003.11:g.10183824A>G genomic True ga4gh:VA.iACeJuNFlj4X2rbHQ2EELvoc3pX9LcaZ +852 NC_000003.11:g.10183822_10183841del genomic True ga4gh:VA.R4ArxouoYlYFOev2VpISs9rHCW6YrtJX +2160 NC_000003.11:g.10183822delC genomic True ga4gh:VA.eSCEkBqaUMJxjt6U6Rpkf4t6DwMAv_wL +1741 NC_000003.11:g.10183823T>C genomic True ga4gh:VA.atSdKibtgfnUf-zpEY_RaFYOY51tX1I0 +2484 NC_000003.11:g.10183823T>A genomic False ga4gh:VA.o6BDmAtfuYAxmT1lToDuIlQch7evUUWT +2480 NC_000003.11:g.10183824A>C genomic False ga4gh:VA.v_VoOAGmvlgQ38aOadJfbGxSwjoNG5Av +3022 NC_000003.11:g.10191943G>A genomic False ga4gh:VA.jyyUcKj9dNzcgO9mmbiNiPrgUeHoLZOR +615 NC_000009.11:g.5070053_5070054insG genomic True ga4gh:VA.Qi5R3HWMYkczdkqe-dmuenUnkV3wqAMa +3161 3-10183878-G-A genomic False ga4gh:VA.teuFANMqHwJET_Cf5GuKKVZNrXR_jqm9 +877 NC_000020.11:g.58903752C>T genomic True ga4gh:VA.NOTqT95mj--g1vgHSIbwKr32mC_vNQBB +731 NC_000003.11:g.37056036G>A genomic True ga4gh:VA.kSZqq7S8DX8XgbimAaP2Lb-V_0DeKiJB +3045 VHL p.F76del protein False ga4gh:VA.92AfH5KBJzL4d38wPE9lfhwRwxD67uZq +4475 MAP2K1 p.K57_G61del protein False ga4gh:VA.S-rGlU9uLFwFZwpH5m4pJ6D0xk9Fe6SJ +3310 HDAC9 p.L33R protein False ga4gh:VA.tH2L9BrPEYGQtFDQhFp_5F6argUBU98T diff --git a/analysis/civic/civic_analysis.ipynb b/analysis/civic/civic_analysis.ipynb new file mode 100644 index 0000000..3094fd7 --- /dev/null +++ b/analysis/civic/civic_analysis.ipynb @@ -0,0 +1,1222 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Analysis for CIViC data\n", + "\n", + "This notebook contains an analysis on CIViC variant data" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/kxk102/.local/share/virtualenvs/variation-normalization-KPVKcmjd/lib/python3.11/site-packages/python_jsonschema_objects/__init__.py:49: UserWarning: Schema version http://json-schema.org/draft-07/schema not recognized. Some keywords and features may not be supported.\n", + " warnings.warn(\n" + ] + } + ], + "source": [ + "import logging\n", + "from enum import Enum\n", + "import re\n", + "import csv\n", + "from pathlib import Path\n", + "import zipfile\n", + "\n", + "from civicpy import civic as civicpy\n", + "from dotenv import load_dotenv\n", + "\n", + "from variation.query import QueryHandler\n", + "\n", + "logging.getLogger(\"root\").setLevel(logging.WARNING)" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Environment variables are set for gene-normalizer dynamodb instance and \n", + "# UTA DB credentials\n", + "load_dotenv()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "query_handler = QueryHandler()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using cache-20230531.pkl.zip for civicpy cache\n" + ] + }, + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Use latest cache that has been pushed to the repo\n", + "latest_cache_zip_path = sorted(Path().glob(\"cache-*.pkl.zip\"))[-1]\n", + "print(f\"Using {latest_cache_zip_path} for civicpy cache\")\n", + "\n", + "with zipfile.ZipFile(latest_cache_zip_path, \"r\") as zip_ref:\n", + " zip_ref.extractall()\n", + "\n", + "civicpy.load_cache(local_cache_path=Path(\"cache.pkl\"), on_stale=\"ignore\")" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'Total Number of variants in CIViC: 3554'" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "variants = civicpy.get_all_variants()\n", + "total_variants = len(variants)\n", + "f\"Total Number of variants in CIViC: {total_variants}\"" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "class VariantCategory(str, Enum):\n", + " \"\"\"Create enum for the kind of variants that are in CIViC.\"\"\"\n", + " EXPRESSION = \"Expression\"\n", + " EPIGENETIC_MODIFICATION = \"Epigenetic Modification\"\n", + " FUSION = \"Fusion\"\n", + " PROTEIN_CONS = \"Protein Consequence\"\n", + " GENE_FUNC = \"Gene Function\"\n", + " REARRANGEMENTS = \"Rearrangements\"\n", + " COPY_NUMBER = \"Copy Number\"\n", + " OTHER = \"Other\"\n", + " GENOTYPES_EASY = \"Genotypes Easy\"\n", + " GENOTYPES_COMPOUND = \"Genotypes Compound\"\n", + " REGION_DEFINED_VAR = \"Region Defined Variant\"\n", + " TRANSCRIPT_VAR = \"Transcript Variant\" # no attempt to normalize these ones, since there is no query we could use\n", + " " + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Transcript Variants we did not attempt to normalize due to no input query available \n", + "These are CIViC Variants where we did not attempt to normalize since we cannot find a \n", + "free text or HGVS-like expression to use. One example would be a CIViC Variant whose \n", + "name has \"c.\" in it. In this case, we want the genomic representative. First, we look at the \n", + "HGVS expressions to find a genomic expression. If there is no genomic HGVS expression, we try using the CIViC representative variant coordinates. If neither exist,\n", + "we do not even attempt to normalize. These are under the Transcript Variant category." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below are terms in CIViC that we know that the variation normalizer cannot support." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "not_supported = {\n", + " VariantCategory.EXPRESSION: {\n", + " \"overexpression\", \"expression\", \"underexpression\", \"serum levels\", \n", + " \"transcription levels\", \"autocrine activation\", \"tnc-l\", \n", + " \"top2a/90\", \"low ratio of vegf165b/vegftotal\", \"lgr5fl\"\n", + " },\n", + " VariantCategory.EPIGENETIC_MODIFICATION: {\n", + " \"methylation\", \"promoter hypermethylation\", \"promoter methylation\", \n", + " \"phosphorylation\"\n", + " },\n", + " VariantCategory.FUSION: {\n", + " \"::\", \"fusion\"\n", + " },\n", + " VariantCategory.PROTEIN_CONS: {\n", + " \"frameshift truncation\", \"frameshift\", \"frame shift\", \"fs\",\n", + " \"truncating mutation\", \"1100delc\", \"deletion (p.k227_t233del)\",\n", + " \"y646f, y646n, y646s, y646h, y646c, a682g, a692v\"\n", + " },\n", + " VariantCategory.GENE_FUNC: {\n", + " \"gain of function\", \"gain-of-function\", \"loss of function\", \"loss-of-function\",\n", + " \"activating mutation\", \"tkd mutation\", \"inactivation\", \"null\", \"viii\"\n", + " },\n", + " VariantCategory.REARRANGEMENTS: {\n", + " \"translocation\", \"rearrangement\", \"double ph\", \"alu insertion\", \n", + " \"exon 20 insertion\", \"internal tandem duplications\", \"tandem repeat\",\n", + " \"itd\", \"d842_h845deldimh\", \"k558np\"\n", + " },\n", + " VariantCategory.COPY_NUMBER: {\n", + " \"copy number\", \"repeat\", \"dup\", \"non-amplification\", \"gain\"\n", + " }, \n", + " VariantCategory.OTHER: {\n", + " \"cytoplasmic mislocalization\", \"alternative transcript\", \"rare mutation\",\n", + " \"splice\", \"splicing\", \"ceacam1-l\", \"ceacam1-s\", \"δ\", # this is really Δ for upper case\n", + " \"delta\", \"beta\", \"ivs2+1g>a\", \"ivs20, a-g, -2\",\n", + " \"deprecated\", \"point mutations\", \"conserved domain mut\", \"cis double mutants\",\n", + " \"loss-of-modification\", \"gbrcam\", \"kras4a\", \"kras4b\", \"e151int\", \"delnvtap\"\n", + " },\n", + " VariantCategory.GENOTYPES_EASY: {\n", + " \"diplotypes\", \"wild type\", \"wildtype\", \"p61braf(v600e)\"\n", + " },\n", + " VariantCategory.GENOTYPES_COMPOUND: {\n", + " \"loss of heterozygosity\", \"biallelic inactivation\", \"bi-allelic inactivation\",\n", + " \"homozygosity\", \"loh\", \"single allele deletion\"\n", + " },\n", + " VariantCategory.REGION_DEFINED_VAR: {\n", + " \"deleterious mutation\", \"domain mutation\", \"polymorphism\", \n", + " \"non-p-loop mutation\", \"p-loop mutation\", \"3' utr mutation\", \"alteration\",\n", + " \"t17 deletion\", \"exon\", \"ex19 del l858r\", \"promoter mutation\", \"non-v600\",\n", + " \"single nucleotide variant\"\n", + " }\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "# This file contains protein queries (gene + variant_name) we SHOULD be able to\n", + "# normalize\n", + "protein_variants_wf = open(\"should_be_able_to_normalize_protein_variant_queries.csv\", \"w\")\n", + "protein_variants_wr = csv.writer(protein_variants_wf, delimiter=\"\\t\")\n", + "protein_variants_wr.writerow([\"variant_id\", \"gene_name\", \"variant_name\", \"variant_accepted\"])\n", + "\n", + "# This file contains genomic queries (genomic HGVS expressions) we SHOULD be able to\n", + "# normalize\n", + "genomic_variants_wf = open(\"should_be_able_to_normalize_genomic_variant_queries.csv\", \"w\")\n", + "genomic_variants_wr = csv.writer(genomic_variants_wf, delimiter=\"\\t\")\n", + "genomic_variants_wr.writerow([\"variant_id\", \"hgvs_g\", \"variant_accepted\"])\n", + "\n", + "# This file contains CIViC Variants we do not currently support in Variation Normalizer.\n", + "# In these cases, we do not even attempt to try to normalize\n", + "not_supported_wf = open(\"not_supported_variants.csv\", \"w\")\n", + "not_supported_wr = csv.writer(not_supported_wf, delimiter=\"\\t\")\n", + "not_supported_wr.writerow([\"variant_id\", \"gene_name\", \"variant_name\", \"category\", \"variant_accepted\"])\n", + "\n", + "# This file contains CIViC Variant queries that we were not able to normalize.\n", + "unable_to_normalize_wf = open(\"unable_to_normalize_queries.csv\", \"w\")\n", + "unable_to_normalize_wr = csv.writer(unable_to_normalize_wf, delimiter=\"\\t\")\n", + "unable_to_normalize_wr.writerow([\"variant_id\", \"query\", \"query_type\", \"variant_accepted\",\n", + " \"exception_raised\", \"message\", \"warnings\"])\n", + "\n", + "# This file contains CIViC Variant queries that we were able to normalize.\n", + "able_to_normalize_wf = open(\"able_to_normalize_queries.csv\", \"w\")\n", + "able_to_normalize_wr = csv.writer(able_to_normalize_wf, delimiter=\"\\t\")\n", + "able_to_normalize_wr.writerow([\"variant_id\", \"query\", \"query_type\", \"variant_accepted\", \"vrs_id\"])\n", + "\n", + "# Category name for variants we do not support: number of variants we found\n", + "variant_category_counts = {c: 0 for c in VariantCategory.__members__}\n", + "\n", + "\n", + "def _total_counts():\n", + " \"\"\"Return initial total counts for genomic and protein variants\"\"\"\n", + " return {\n", + " \"protein\": {\"accepted\": 0, \"not_accepted\": 0, \"count\": 0}, \n", + " \"genomic\": {\"accepted\": 0, \"not_accepted\": 0, \"count\": 0}\n", + " }\n", + "\n", + "# Keep track of total counts\n", + "should_be_able_to_normalize_total = _total_counts()\n", + "can_normalize_total = _total_counts()\n", + "unable_to_normalize_total = _total_counts()\n", + "exception_total = _total_counts()\n", + "\n", + "queries_found = dict()\n", + "\n", + "def is_accepted_variant(v) -> bool:\n", + " \"\"\"Return whether or not a variant (MP) has at least one EID in an accepted status.\"\"\" \n", + " for mp in v.molecular_profiles:\n", + " for ev in mp.evidence_items:\n", + " if ev.status == \"accepted\":\n", + " return True\n", + " return False\n", + "\n", + "for variant in variants:\n", + " v_name = None\n", + " v_q_type = None\n", + "\n", + " # if a variant has at least one EID in an accepted status, it counts towards \n", + " # “accepted”, because that indicates review and approval of the variant as part \n", + " # of the evidence review\n", + " is_accepted = is_accepted_variant(variant)\n", + " accepted_key = \"accepted\" if is_accepted else \"not_accepted\" # used in total counts dicts\n", + " \n", + " if \"c.\" in variant.name:\n", + " # Try getting genomic HGVS expression first\n", + " v_name = ([expr for expr in variant.hgvs_expressions \n", + " if \"g.\" in expr] or [None])[0]\n", + "\n", + " # If there is no genomic HGVS expression, try using gnomad vcf\n", + " if not v_name:\n", + " chromosome = variant.coordinates.chromosome\n", + " pos = variant.coordinates.start\n", + " ref = variant.coordinates.reference_bases\n", + " alt = variant.coordinates.variant_bases\n", + "\n", + " if all((chromosome, pos, ref, alt)):\n", + " v_name = f\"{chromosome}-{pos}-{ref}-{alt}\"\n", + " \n", + " v_q_type = \"genomic\"\n", + " else:\n", + " v_name = variant.name.strip()\n", + " v_q_type = \"protein\"\n", + "\n", + " gene_name = variant.gene.name.strip()\n", + " \n", + " if not v_name:\n", + " variant_category_name = VariantCategory.TRANSCRIPT_VAR\n", + " variant_category_counts[variant_category_name.name] += 1 \n", + " not_supported_wr.writerow([variant.id, gene_name, None, variant_category_name, is_accepted])\n", + " continue\n", + "\n", + " v_name_lower = v_name.lower()\n", + " \n", + " categories = set()\n", + " if v_name_lower in {\"loss\", \"deletion\"}:\n", + " categories.add(VariantCategory.GENE_FUNC)\n", + " elif any((\n", + " v_name_lower in {\"mutation\", \"mutations\", \"snp\"},\n", + " v_name_lower == f\"{variant.gene.name.lower()} mutation\"\n", + " )):\n", + " categories.add(VariantCategory.REGION_DEFINED_VAR)\n", + " else:\n", + " if v_name_lower.endswith(\"deletion and mutation\"):\n", + " v_name_split = v_name.split()\n", + " if len(v_name_split) == 4:\n", + " if query_handler.normalize_handler.gene_normalizer.normalize(v_name_split[0]).match_type > 0:\n", + " categories.add(VariantCategory.REGION_DEFINED_VAR) \n", + " \n", + " if re.match(r\".*e\\d+-e\\d+\", v_name_lower): # ex: e20-e20\n", + " categories.add(VariantCategory.FUSION)\n", + "\n", + " if any((\n", + " \"exon\" in v_name_lower,\n", + " re.match(r\"\\d+kb\\sdeletion\", v_name_lower), # ex: 10kb Deletion\n", + " re.match(r\"partial\\sdeletion\\sof\\s\\d+(.\\d+)?\\skb\", v_name_lower), # ex: Partial deletion of 0.7 Kb\n", + " re.match(r\"del\\s\\d+-\\d+\", v_name_lower), # ex: DEL 485-490\n", + " re.match(r\"\\d+(p|q)\\d+(.\\d+)?-\\d+(.\\d+)?\\s\\d+mb del\", v_name_lower), # ex: 3p26.3-25.3 11Mb del\n", + " re.match(r\"intron\\s\\d+\\smutation\", v_name_lower) # ex: Intron 6 Mutation\n", + " )):\n", + " categories.add(VariantCategory.REGION_DEFINED_VAR)\n", + " \n", + " if any((\n", + " re.match(r\"t\\(.*\\)\\(.*\\)\", v_name_lower), # ex: t(1;3)(p36.3;p25)\n", + " re.match(r\".*ins$\", v_name_lower), # ex: P780INS, L78_Q79ins\n", + " re.match(r\"\\w+_?\\w+>\\w+\", v_name_lower), # ex: 56_61QKQKVG>R, E746_T751>I, N771>GY\n", + " )): \n", + " categories.add(VariantCategory.REARRANGEMENTS)\n", + "\n", + " if any((\n", + " re.match(r\"^rs\\d+\", v_name_lower), # ex: RS11623866\n", + " re.match(r\"class\\s\\d+\\smutation\", v_name_lower), # ex: Class 3 Mutation\n", + " re.match(r\"\\d+\\s\\((c|a|g|t)+-(c|a|g|t)+\\)\", v_name_lower) # ex: 235 (CAG-TAG)\n", + " )):\n", + " categories.add(VariantCategory.OTHER)\n", + "\n", + " if re.match(r\"cd\\d+v?\\d+\", v_name_lower):\n", + " categories.add(VariantCategory.EXPRESSION)\n", + "\n", + " if any((\n", + " re.match(r\"\\w+\\d+$\", v_name_lower), # ex: V600\n", + " re.match(r\"\\w+\\d+\\w+\\/\\w+$\", v_name_lower), # ex: S893A/T\n", + " re.match(r\"[a-z]+\\d+[a-z]+\\sand\\s[a-z]+\\d+[a-z|*]+\", v_name_lower), # ex: E2014K and E2419K, R849W and R1108*\n", + " re.match(r\"[a-z]+\\d+\\s&\\s[a-z]+\\d+\", v_name_lower), # ex: D835 & I836\n", + " re.match(r\"[a-z]+\\d+[a-z]+\\sor\\s[a-z]+\\d+[a-z]+\", v_name_lower), # ex: H1047L or H1047R\n", + " re.match(r\"\\w+\\d+\\smutations\", v_name_lower), # ex: E1813 mutations\n", + " )):\n", + " categories.add(VariantCategory.PROTEIN_CONS)\n", + "\n", + " if any((\n", + " re.match(r\"^\\w+\\samplification\", v_name_lower), # ex: {gene} amplification\n", + " re.match(r\"grch3(7|8)\\/hg\\d+\\s\\w+.?\\d*\\(chr\\w+:\\d+-\\d+\\)x\\d+\", v_name_lower), # ex: GRCh37/hg19 11q14.3(chr11:88960991-88961138)x160\n", + " )): \n", + " categories.add(VariantCategory.COPY_NUMBER)\n", + "\n", + " if re.match(r\"\\w+[^fs]\\*\\d+$\", v_name_lower): # ex: UGT1A1*28\n", + " categories.add(VariantCategory.GENOTYPES_EASY)\n", + "\n", + " for k, v in not_supported.items():\n", + " if {x for x in v if x in v_name_lower}:\n", + " categories.add(k)\n", + "\n", + " if len(categories) > 1:\n", + " # Those with multiple categories will be classified as other\n", + " categories = {VariantCategory.OTHER}\n", + "\n", + " if len(categories) == 1:\n", + " variant_category_name = categories.pop()\n", + " variant_category_counts[variant_category_name.name] += 1\n", + " not_supported_wr.writerow([variant.id, gene_name, variant.name, variant_category_name, is_accepted])\n", + " else:\n", + " # We should support this, so we need to query the variation normalizer\n", + " if v_q_type == \"protein\":\n", + " q = f\"{gene_name} {v_name}\"\n", + " protein_variants_wr.writerow([variant.id, gene_name, v_name, is_accepted])\n", + " else:\n", + " q = v_name\n", + " genomic_variants_wr.writerow([variant.id, q, is_accepted])\n", + "\n", + " should_be_able_to_normalize_total[v_q_type][\"count\"] += 1\n", + " should_be_able_to_normalize_total[v_q_type][accepted_key] += 1\n", + "\n", + " if q in queries_found:\n", + " queries_found[q].append(variant.id)\n", + " else:\n", + " queries_found[q] = [variant.id]\n", + " \n", + " try:\n", + " variation_norm_resp = await query_handler.normalize_handler.normalize(q)\n", + " if not variation_norm_resp.variation_descriptor:\n", + " is_incomplete = False\n", + " if v_q_type == \"protein\" and len(v_name.split()) == 1:\n", + " if \"-\" in v_name:\n", + " # could be {gene}-{gene}\n", + " genes = v_name.split(\"-\")\n", + " variant_category_name = VariantCategory.FUSION\n", + " else:\n", + " # Just a gene name\n", + " genes = [v_name]\n", + " variant_category_name = VariantCategory.OTHER\n", + "\n", + " is_genes = True\n", + " for g in genes:\n", + " if query_handler.normalize_handler.gene_normalizer.normalize(g).match_type == 0:\n", + " # not a gene \n", + " is_genes = False\n", + " break\n", + "\n", + " if is_genes:\n", + " variant_category_counts[variant_category_name.name] += 1\n", + " not_supported_wr.writerow([variant.id, gene_name, variant.name, variant_category_name, is_accepted])\n", + " is_incomplete = True\n", + "\n", + " if not is_incomplete:\n", + " unable_to_normalize_wr.writerow([variant.id, q, v_q_type, \n", + " is_accepted, False,\n", + " \"unable to normalize\",\n", + " variation_norm_resp.warnings])\n", + " unable_to_normalize_total[v_q_type][\"count\"] += 1\n", + " unable_to_normalize_total[v_q_type][accepted_key] += 1\n", + " else:\n", + " can_normalize_total[v_q_type][\"count\"] += 1\n", + " can_normalize_total[v_q_type][accepted_key] += 1\n", + " vrs_id = variation_norm_resp.variation_descriptor.variation.id\n", + " able_to_normalize_wr.writerow([variant.id, q, v_q_type, is_accepted, vrs_id])\n", + " except Exception as e:\n", + " unable_to_normalize_wr.writerow([variant.id, q, v_q_type, is_accepted,\n", + " True, str(e), None])\n", + " exception_total[v_q_type][\"count\"] += 1\n", + " exception_total[v_q_type][accepted_key] += 1\n", + "\n", + "# Close all files\n", + "protein_variants_wf.close()\n", + "genomic_variants_wf.close()\n", + "not_supported_wf.close()\n", + "unable_to_normalize_wf.close()\n", + "able_to_normalize_wf.close()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Variants we do not support" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "do_not_support_total_sum = sum(variant_category_counts.values())" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below are the total number of variants for each category that we do not support" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'TRANSCRIPT_VAR': 385,\n", + " 'FUSION': 308,\n", + " 'EXPRESSION': 291,\n", + " 'REGION_DEFINED_VAR': 209,\n", + " 'PROTEIN_CONS': 128,\n", + " 'OTHER': 93,\n", + " 'GENE_FUNC': 90,\n", + " 'REARRANGEMENTS': 52,\n", + " 'COPY_NUMBER': 34,\n", + " 'EPIGENETIC_MODIFICATION': 15,\n", + " 'GENOTYPES_EASY': 11,\n", + " 'GENOTYPES_COMPOUND': 6}" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sorted_variant_cat_counts = dict(sorted(variant_category_counts.items(), key=lambda x: x[1], reverse=True))\n", + "sorted_variant_cat_counts" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below is the total percentage of variants for each category that we do not support" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'TRANSCRIPT_VAR': '10.83%',\n", + " 'FUSION': '8.67%',\n", + " 'EXPRESSION': '8.19%',\n", + " 'REGION_DEFINED_VAR': '5.88%',\n", + " 'PROTEIN_CONS': '3.60%',\n", + " 'OTHER': '2.62%',\n", + " 'GENE_FUNC': '2.53%',\n", + " 'REARRANGEMENTS': '1.46%',\n", + " 'COPY_NUMBER': '0.96%',\n", + " 'EPIGENETIC_MODIFICATION': '0.42%',\n", + " 'GENOTYPES_EASY': '0.31%',\n", + " 'GENOTYPES_COMPOUND': '0.17%'}" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "{k: f\"{v / total_variants * 100:.2f}%\" for k, v in sorted_variant_cat_counts.items()}" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer does not support 45.64% of the total variants'" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer does not support {do_not_support_total_sum / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'Total number of variants we do not support in the Variation Normalizer: 1622'" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"Total number of variants we do not support in the Variation Normalizer: \"\\\n", + "f\"{do_not_support_total_sum}\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Variants we should be able to normalize" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'protein': {'accepted': 632, 'not_accepted': 881, 'count': 1513},\n", + " 'genomic': {'accepted': 245, 'not_accepted': 180, 'count': 425}}" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "should_be_able_to_normalize_total" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1938" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "should_be_able_to_normalize_total_sum = should_be_able_to_normalize_total[\"protein\"][\"count\"] + should_be_able_to_normalize_total[\"genomic\"][\"count\"]\n", + "should_be_able_to_normalize_total_sum" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'45.25% of these are accepted variants'" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "should_be_able_to_normalize_total_accepted = should_be_able_to_normalize_total[\"protein\"][\"accepted\"] + should_be_able_to_normalize_total[\"genomic\"][\"accepted\"]\n", + "f\"{should_be_able_to_normalize_total_accepted / should_be_able_to_normalize_total_sum * 100:.2f}% of these are accepted variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'54.75% of these are NOT accepted variants'" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "should_be_able_to_normalize_total_not_accepted = should_be_able_to_normalize_total[\"protein\"][\"not_accepted\"] + should_be_able_to_normalize_total[\"genomic\"][\"not_accepted\"]\n", + "f\"{should_be_able_to_normalize_total_not_accepted / should_be_able_to_normalize_total_sum * 100:.2f}% of these are NOT accepted variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer SHOULD be able to normalize 54.53% of the total variants'" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer SHOULD be able to normalize {should_be_able_to_normalize_total_sum / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Variants we were not able to normalize\n", + "\n", + "Either due to a bug or an unsupported query type in Variation Normalizer" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'protein': {'accepted': 8, 'not_accepted': 52, 'count': 60},\n", + " 'genomic': {'accepted': 1, 'not_accepted': 2, 'count': 3}}" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "unable_to_normalize_total" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "63" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "unable_to_normalize_total_sum = unable_to_normalize_total[\"protein\"][\"count\"] + unable_to_normalize_total[\"genomic\"][\"count\"]\n", + "unable_to_normalize_total_sum" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'14.29% of these are accepted variants'" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "unable_to_normalize_total_accepted = unable_to_normalize_total[\"protein\"][\"accepted\"] + unable_to_normalize_total[\"genomic\"][\"accepted\"]\n", + "f\"{unable_to_normalize_total_accepted / unable_to_normalize_total_sum * 100:.2f}% of these are accepted variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'85.71% of these are NOT accepted variants'" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "unable_to_normalize_total_not_accepted = unable_to_normalize_total[\"protein\"][\"not_accepted\"] + unable_to_normalize_total[\"genomic\"][\"not_accepted\"]\n", + "f\"{unable_to_normalize_total_not_accepted / unable_to_normalize_total_sum * 100:.2f}% of these are NOT accepted variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer was unable to normalize 1.77% of the total variants'" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer was unable to normalize {unable_to_normalize_total_sum / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Breakdown of the variants we weren't able to normalize\n", + "\n", + "In this section, we breakdown the reasons on why we weren't able to normalize variants." + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [], + "source": [ + "unable_to_tokenize = 0\n", + "unable_to_find_valid = 0\n", + "other = 0\n", + "with open(\"unable_to_normalize_queries.csv\", \"r\") as f:\n", + " reader = csv.reader(f, delimiter=\"\\t\")\n", + " next(reader)\n", + " for row in reader:\n", + " if \"Unable to find valid result\" in row[-1]:\n", + " unable_to_find_valid += 1\n", + " elif \"Unable to tokenize\" in row[-1]:\n", + " unable_to_tokenize += 1\n", + " else:\n", + " other += 1" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Due to not passing validation checks\n", + "\n", + "The Variation Normalizer performs validation checks on the input query (such as reference sequence). If these validation checks fail, then the input query will fail to normalize." + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer found 62 invalid variants (This is 1.74% of the total variants).'" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer found {unable_to_find_valid} invalid variants (This is {unable_to_find_valid / total_variants * 100:.2f}% of the total variants).\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Due to tokenization \n", + "\n", + "The Variation Normalizer will tokenize the input query to determine the kind of token. It is limited in the kinds of tokens it accepts, so these tokens are not yet supported in the Variation Normalizer. " + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer was unable to tokenize 1 variants (0.03% of the total variants).'" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer was unable to tokenize {unable_to_tokenize} variants ({unable_to_tokenize / total_variants * 100:.2f}% of the total variants).\"" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer was unable to normalize 0 variants due to other issues (This is 0.00% of the total variants).'" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer was unable to normalize {other} variants due to other issues (This is {other / total_variants * 100:.2f}% of the total variants).\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Variant queries that raised an exception during normalization" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'protein': {'accepted': 0, 'not_accepted': 0, 'count': 0},\n", + " 'genomic': {'accepted': 0, 'not_accepted': 0, 'count': 0}}" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "exception_total" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "exception_total_sum = exception_total[\"protein\"][\"count\"] + exception_total[\"genomic\"][\"count\"]\n", + "exception_total_sum" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer raised an exception for 0.00% of the total variants'" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer raised an exception for {exception_total_sum / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Variants we were able to normalize" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'protein': {'accepted': 622, 'not_accepted': 825, 'count': 1447},\n", + " 'genomic': {'accepted': 244, 'not_accepted': 178, 'count': 422}}" + ] + }, + "execution_count": 31, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "can_normalize_total" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1869" + ] + }, + "execution_count": 32, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "can_normalize_total_sum = can_normalize_total[\"protein\"][\"count\"] + can_normalize_total[\"genomic\"][\"count\"]\n", + "can_normalize_total_sum" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'46.33% of these are accepted variants'" + ] + }, + "execution_count": 33, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "can_normalize_total_accepted = can_normalize_total[\"protein\"][\"accepted\"] + can_normalize_total[\"genomic\"][\"accepted\"]\n", + "f\"{can_normalize_total_accepted / can_normalize_total_sum * 100:.2f}% of these are accepted variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'53.67% of these are NOT accepted variants'" + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "can_normalize_total_not_accepted = can_normalize_total[\"protein\"][\"not_accepted\"] + can_normalize_total[\"genomic\"][\"not_accepted\"]\n", + "f\"{can_normalize_total_not_accepted / can_normalize_total_sum * 100:.2f}% of these are NOT accepted variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer successfully normalized 96.44% of the variants we SHOULD be able to normalize'" + ] + }, + "execution_count": 35, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer successfully normalized {can_normalize_total_sum / should_be_able_to_normalize_total_sum * 100:.2f}% of the variants we SHOULD be able to normalize\"" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer successfully normalized 52.59% of the total variants'" + ] + }, + "execution_count": 36, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer successfully normalized {can_normalize_total_sum / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Duplicate Queries\n", + "\n", + "These are duplicate queries found in civic. The values are the associated variant IDs. " + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'BRAF V600D': [11, 3452], 'BRAF V600R': [16, 991]}" + ] + }, + "execution_count": 37, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "{k:v for k,v in queries_found.items() if len(v) > 1}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "variation-normalization-KPVKcmjd", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.3" + }, + "orig_nbformat": 4, + "vscode": { + "interpreter": { + "hash": "0be8ba9a7b89517724a412b9d40e184059795303560bd1108143a8aed13113be" + } + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/analysis/civic/not_supported_variants.csv b/analysis/civic/not_supported_variants.csv new file mode 100644 index 0000000..1549a9d --- /dev/null +++ b/analysis/civic/not_supported_variants.csv @@ -0,0 +1,1623 @@ +variant_id gene_name variant_name category variant_accepted +4170 VHL Transcript Variant False +4417 ALK FBXO11::ALK Fusion False +4214 VHL Transcript Variant False +4216 VHL Transcript Variant False +4278 VHL Transcript Variant False +4232 BRCA1 Transcript Variant False +3196 VHL Transcript Variant False +2930 VHL Transcript Variant True +4188 VHL 10kb Deletion Region Defined Variant False +785 CHEK2 1100DELC Protein Consequence True +3083 VHL Transcript Variant False +2438 VHL 235 (CAG-TAG) Other False +4186 VHL 2kb Deletion Region Defined Variant False +823 EPCAM 3' Exon Deletion Region Defined Variant True +253 EGFR 3' UTR MUTATION Region Defined Variant False +433 HIF1A 3' UTR Polymorphism Region Defined Variant True +3102 VHL Transcript Variant False +2367 VHL 3p26.3-25.3 11Mb del Region Defined Variant True +265 TYMS 5' TANDEM REPEAT Other True +2390 MAP2K1 56_61QKQKVG>R Rearrangements False +4187 VHL 5kb Deletion Region Defined Variant False +2727 ERBB2 A129 Protein Consequence False +2729 TP53 A129 Protein Consequence False +2979 KRAS A146 Protein Consequence True +3195 VHL A149fs (c.444dup) Copy Number False +2482 VHL Transcript Variant False +2023 VHL Transcript Variant True +2962 RUNX1 Transcript Variant False +2442 VHL Transcript Variant False +2265 VHL Transcript Variant True +2144 VHL A56fs (c.166dup) Copy Number True +1579 EGFR A767_V769dupASV Copy Number True +780 GLI1 ACTB::GLI1 Fusion True +3702 NTRK2 AFAP1::NTRK2 Fusion True +2577 PDGFRB AGGF1::PDGFRB C843G Fusion False +285 BRAF AGK::BRAF Fusion True +184 BRAF AKAP9::BRAF Fusion True +1307 TP53 ALTERATION Region Defined Variant True +2211 BAP1 ALTERNATIVE TRANSCRIPT (ATI) Other True +842 BRAF APC Other False +2772 NRG1 APP::NRG1 Fusion True +3460 AR AR alternative transcripts Other False +3622 TFE3 ASPSCR1::TFE3 Fusion False +2846 JAK2 ATF7IP::JAK2 Fusion True +2632 PDGFRB ATF7IP::PDGFRB Fusion False +2758 BRCA1 ATM Other False +2178 NRG1 ATP1B1::NRG1 Fusion True +309 EGFR AUTOCRINE ACTIVATION Expression False +1296 CTNNB1 Activating Mutation Gene Function True +2649 KRAS Activating Mutation Gene Function False +2657 ERBB2 Activating Mutation Gene Function False +3737 EZH2 Activating Mutation Gene Function True +839 ALK Alternative Transcript (ATI) Other True +3510 BCL2L11 Alternative splicing Other False +709 BRCA1 Alu insertion Rearrangements True +461 PML B2 DOMAIN MUTATION Region Defined Variant True +3312 FGFR1 BAG4::FGFR1 Fusion False +3251 BCOR BCOR::CCNB3 Fusion False +1 ABL1 BCR::ABL Fusion True +1607 ABL1 BCR::ABL A365V Fusion False +1608 ABL1 BCR::ABL A366G Fusion False +1612 ABL1 BCR::ABL A397P Fusion True +1027 ABL1 BCR::ABL D276G Fusion True +2900 ABL1 BCR::ABL D363G Fusion True +1532 ABL1 BCR::ABL D421G Fusion True +2890 ABL1 BCR::ABL E255K V299L Fusion True +1173 ABL1 BCR::ABL E255V Fusion True +1526 ABL1 BCR::ABL E279K Fusion True +2886 ABL1 BCR::ABL E279K Fusion True +2887 ABL1 BCR::ABL E292L Fusion True +1183 ABL1 BCR::ABL E292V Fusion True +1487 ABL1 BCR::ABL E355G Fusion True +2948 ABL1 BCR::ABL E450Q Fusion True +1534 ABL1 BCR::ABL E450V Fusion True +1536 ABL1 BCR::ABL E453A Fusion True +1535 ABL1 BCR::ABL E453K Fusion True +1509 ABL1 BCR::ABL E453Q Fusion True +2370 ABL1 BCR::ABL E459K Fusion True +2901 ABL1 BCR::ABL E98G Fusion True +1528 ABL1 BCR::ABL F311L Fusion True +2358 ABL1 BCR::ABL F311V Fusion False +2359 ABL1 BCR::ABL F317C Fusion True +1625 ABL1 BCR::ABL F317I Fusion True +2888 ABL1 BCR::ABL F317R Fusion True +2343 ABL1 BCR::ABL F317S Fusion True +1184 ABL1 BCR::ABL F359C Fusion True +1523 ABL1 BCR::ABL F359I Fusion True +892 ABL1 BCR::ABL F359V Fusion True +1152 ABL1 BCR::ABL F486S Fusion True +1023 ABL1 BCR::ABL G250E Fusion True +1233 ABL1 BCR::ABL G398R Fusion True +1531 ABL1 BCR::ABL H396P Fusion True +1030 ABL1 BCR::ABL H396R Fusion True +1533 ABL1 BCR::ABL I432T Fusion False +2340 ABL1 BCR::ABL L248R Fusion True +2889 ABL1 BCR::ABL L248R and F359I Fusion True +1022 ABL1 BCR::ABL L248V Fusion True +2902 ABL1 BCR::ABL L364I Fusion True +1530 ABL1 BCR::ABL L364P Fusion True +1230 ABL1 BCR::ABL L384M Fusion True +1232 ABL1 BCR::ABL L387F Fusion True +1488 ABL1 BCR::ABL L387M Fusion True +1021 ABL1 BCR::ABL M244V Fusion True +2949 ABL1 BCR::ABL M244V and L364I Fusion True +1524 ABL1 BCR::ABL M343T Fusion True +1029 ABL1 BCR::ABL M351T Fusion True +2954 ABL1 BCR::ABL M388L Fusion True +2951 ABL1 BCR::ABL N146S Fusion True +1529 ABL1 BCR::ABL N331S Fusion True +1640 ABL1 BCR::ABL N336S Fusion True +2950 ABL1 BCR::ABL N49S Fusion False +1537 ABL1 BCR::ABL P480A Fusion True +1024 ABL1 BCR::ABL Q252H Fusion True +1600 ABL1 BCR::ABL Q252R Fusion False +1527 ABL1 BCR::ABL Q300R Fusion True +1613 ABL1 BCR::ABL S417Y Fusion True +2953 ABL1 BCR::ABL S438C Fusion True +2335 ABL1 BCR::ABL T315A Fusion True +4508 ABL1 BCR::ABL T315I Fusion False +2885 ABL1 BCR::ABL T315V Fusion True +2903 ABL1 BCR::ABL V186A Fusion False +2952 ABL1 BCR::ABL V298I Fusion True +1231 ABL1 BCR::ABL V299L Fusion True +1609 ABL1 BCR::ABL V379I Fusion True +1026 ABL1 BCR::ABL Y253F Fusion True +2909 ABL1 BCR::ABL Y253F Fusion True +1025 ABL1 BCR::ABL Y253H Fusion True +4467 ABL1 BCR::ABL mutations Fusion False +4497 FGFR1 BCR::FGFR1 Fusion False +2860 JAK2 BCR::JAK2 Fusion True +2971 PDGFRA BCR::PDGFRA Fusion True +594 CEBPA BIALLELIC INACTIVATION Other True +656 BRAF BRAF::CUL1 Fusion True +719 BRD4 BRD4::NUTM1 Fusion True +532 PALB2 Biallelic Inactivation Other True +2391 MAP2K1 C121S and G128D Protein Consequence False +3170 VHL Transcript Variant False +4181 VHL Transcript Variant False +4108 VHL Transcript Variant False +2132 VHL C77fs (c.228dup) Copy Number True +3245 VHL Transcript Variant True +2769 ALK CAD::ALK Fusion True +2630 CBFA2T3 CBFA2T3::GLIS2 Fusion False +431 CBFB CBFB::MYH11 Fusion True +626 RET CCDC6::RET Fusion True +3385 CD44 CD44s Expression False +341 CD44 CD44s Expression Expression True +3386 CD44 CD44v5 and CD44v6 Expression False +3373 CD44 CD44v6 Other True +3388 CD44 CD44v6 and CD44v10 Expression False +3387 CD44 CD44v6+/CD44s- Expression False +3369 CD44 CD44v8-10 Expression False +3368 CD44 CD44v9 Other False +3367 CD44 CD4v8-v10 and CD44v3-v10 Expression False +2771 NRG1 CD74::NRG1 Other False +465 ROS1 CD74::ROS1 G2032R Other True +518 ROS1 CD74::ROS1 G2101A Other True +516 ROS1 CD74::ROS1 L2026M Other True +517 ROS1 CD74::ROS1 L2155S Other True +3474 CEACAM1 CEACAM1-L Other False +3475 CEACAM1 CEACAM1-S Other False +3270 ABL1 CENPC::ABL1 Fusion True +3252 CIC CIC::DUX4 Fusion False +3987 CIC CIC::LEUTX Fusion False +520 ALK CLTC::ALK Fusion True +3991 PDGFB COL1A1-PDGFB fusion Fusion True +2972 PDGFB COL1A1::PDGFB Fusion True +1300 TP53 CONSERVED DOMAIN MUT Other True +821 HLA-C COPY-NEUTRAL LOSS OF HETEROZYGOSITY Genotypes Compound True +599 CTLA4 CTLA4::CD28 Fusion True +2229 BRAF CUX1::BRAF Fusion True +447 FGF13 CYTOPLASMIC EXPRESSION Expression True +1283 CDK2 CYTOPLASMIC EXPRESSION Expression False +360 CDKN1B CYTOPLASMIC MISLOCALIZATION Other True +3408 TEK Cis double mutants Other False +2800 BRAF Class 2 Mutations Other False +2801 BRAF Class 3 Mutations Other False +191 EGFR Copy Number Variation Copy Number True +3567 VHL Transcript Variant False +2553 VHL Transcript Variant True +3156 VHL Transcript Variant False +1918 VHL Transcript Variant True +3179 VHL Transcript Variant False +4207 VHL Transcript Variant False +4153 VHL Transcript Variant False +1844 VHL Transcript Variant True +2734 TP53 D184 Protein Consequence False +2479 VHL Transcript Variant False +3260 VHL Transcript Variant False +2767 BRAF D594 Protein Consequence False +746 MLH1 D667FS Protein Consequence True +2673 EPHB2 Transcript Variant False +437 FLT3 D835 Protein Consequence True +3231 FLT3 D835 & I836 Protein Consequence False +613 FLT3 D835H/Y Protein Consequence True +943 PDGFRA D842_H845DELDIMH Rearrangements True +3360 VHL Transcript Variant False +2963 RUNX1 Transcript Variant False +4495 ALK DCTN1::ALK Fusion False +2394 NTRK1 DDR2::NTRK1 Fusion True +2706 DEK DEK::AFF2 Fusion False +522 BRAF DEL 485-490 Region Defined Variant True +954 KIT DEL 554-558 Region Defined Variant False +647 LRP1B DELETION Gene Function True +1663 BRAF DELNVTAP Other False +2685 DGKH DGKH::ZFAND3 Fusion False +242 TP53 DNA Binding Domain Mutation Region Defined Variant True +31 PRKACA DNAJB1::PRKACA Fusion True +738 DPYD DPYD*13 HOMOZYGOSITY Genotypes Compound True +737 DPYD DPYD*2A HOMOZYGOSITY Genotypes Compound True +2589 DUX4 DUX4::IGH Fusion False +3509 AIMP2 DX2 Protein Consequence False +334 VEGFA Decreased Peri-therapeutic Expression Expression True +221 TP53 Deleterious Mutation Region Defined Variant True +200 IKZF1 Deletion Gene Function True +213 PTEN Deletion Gene Function True +250 GSTP1 Deletion Gene Function True +646 SMAD4 Deletion Gene Function True +696 SMARCB1 Deletion Gene Function True +856 CREBBP Deletion Gene Function False +1982 SUFU Deletion Gene Function False +1983 PTCH1 Deletion Gene Function False +2654 CDKN2A Deletion Gene Function True +2932 VHL Deletion Gene Function True +3309 ATRX Deletion Gene Function True +4314 CDKN2B Deletion Gene Function False +4316 PAX5 Deletion Gene Function False +4317 ERG Deletion Gene Function False +4479 BRCA2 Deletion Gene Function False +4480 TP53 Deletion Gene Function False +4192 VHL Transcript Variant False +4193 VHL Transcript Variant False +4194 VHL Transcript Variant False +526 BCL2L11 Deletion Polymorphism Region Defined Variant True +3009 ABL1 Double Ph Rearrangements True +725 MLH1 E13fs Protein Consequence True +2994 MAEA E151INT Other False +4155 VHL Transcript Variant False +2591 DICER1 E1813 mutations Protein Consequence False +2529 VHL Transcript Variant False +2730 TP53 E204 Protein Consequence False +4234 VHL Transcript Variant False +763 MSH2 E28FS Protein Consequence True +4275 VHL Transcript Variant False +3383 VHL Transcript Variant False +1735 VHL Transcript Variant False +2763 PIK3CA E545 Protein Consequence True +3635 VHL Transcript Variant False +4077 VHL Transcript Variant False +2301 VHL Transcript Variant False +3744 VHL Transcript Variant False +3654 VHL Transcript Variant False +3328 FLT3 E573Δ Other False +1544 FLT3 E611_F612INS25 Protein Consequence False +2258 EGFR E709A and G719C Protein Consequence False +2256 EGFR E709K and G719A Protein Consequence False +1577 EGFR E709_T710>D Rearrangements False +3036 VHL Transcript Variant False +2538 VHL Transcript Variant False +2304 VHL Transcript Variant False +4161 VHL Transcript Variant False +1635 EGFR E746_A750>IP Rearrangements False +1433 EGFR E746_S752>A Rearrangements False +1003 EGFR E746_T751>I Rearrangements True +2310 VHL Transcript Variant False +2847 JAK2 EBF1::JAK2 Fusion True +535 PDGFRB EBF1::PDGFRB Fusion True +3484 FN1 EDB Other False +4270 EGFR EGFR ITD Rearrangements False +4294 EGFR EGFR::BRAF Fusion False +4283 EGFR EGFR::PPARGC1A Fusion False +4282 EGFR EGFR::PURB Fusion False +2203 EGFR EGFR::RAD51 Fusion True +4241 EGFR EGFR::SEPT14 Fusion True +4343 EGFR EGFR::VSTM2A Fusion False +4344 EGFR EGFR::WIF1 Fusion False +4418 EGFR EGFR::YAP1 Fusion False +4286 EGFR EGFR::ZNF713 Fusion False +4447 EGFR EGFR::ZNF880 Fusion False +1516 EGFR EGFRVIII Gene Function False +5 ALK EML4::ALK Fusion True +501 ALK EML4::ALK e2-e20 Fusion True +500 ALK EML4::ALK e20-e20 Fusion True +3204 ALK EML4::ALK e6-e19 Fusion False +503 ALK EML4::ALK e6-e20 Fusion True +4020 EML4 EML4::NTRK3 Fusion False +4299 NTRK3 EML4::NTRK3 Fusion False +2750 ALK EML6::ALK Fusion False +4075 EML6 EML6::NTRK3 Fusion False +2670 EPHB2 EPHB2 Protein Consequence False +4308 ALK ERC1::ALK Fusion False +2575 ABL1 ETV6::ABL1 Fusion True +2859 JAK2 ETV6::JAK2 Fusion True +3700 NTRK1 ETV6::NTRK1 Fusion True +2396 NTRK2 ETV6::NTRK2 Fusion True +801 NTRK3 ETV6::NTRK3 Fusion True +805 NTRK3 ETV6::NTRK3 G623R Fusion True +3140 ETV6 ETV6::RUNX1 Fusion True +4005 EWSR1 EWSR1-ERG Fusion False +3054 EWSR1 EWSR1::ATF1 Fusion False +717 DDIT3 EWSR1::DDIT3 Fusion True +194 ERG EWSR1::ERG Fusion True +706 EWSR1 EWSR1::FLI1 Fusion True +164 FLI1 EWSR1::FLI1 e7-e6 Fusion True +2385 EWSR1 EWSR1::NR4A3 Fusion False +2941 EWSR1 EWSR1::WT1 Fusion False +2472 VHL EXON 1-2 DELETION and BRK1 DELETION Region Defined Variant False +303 STK11 EXON 1-2 MUTATION Region Defined Variant True +2893 DPYD EXON 11-19 DELETION Region Defined Variant True +86 NPM1 EXON 12 MUTATION Region Defined Variant True +557 ASXL1 EXON 12 MUTATION Region Defined Variant True +266 LRP1B EXON 12-22 DELETION Region Defined Variant True +74 KRAS EXON 2 Mutations Region Defined Variant False +1940 VHL EXON 2-3 DELETION Region Defined Variant True +559 CALR EXON 9 FRAMESHIFT Other True +25 CDK4 EXPRESSION Expression True +57 GATA2 EXPRESSION Expression True +158 AURKA EXPRESSION Expression True +182 BAP1 EXPRESSION Expression True +278 AKT2 EXPRESSION Expression True +316 TGFA EXPRESSION Expression True +318 EREG EXPRESSION Expression True +319 EFNA2 EXPRESSION Expression False +326 CBLC EXPRESSION Expression True +328 DEFA1 EXPRESSION Expression True +335 DNMT1 EXPRESSION Expression True +337 PDCD4 EXPRESSION Expression True +339 TFF3 EXPRESSION Expression True +342 EGF EXPRESSION Expression True +343 MDM2 EXPRESSION Expression True +344 HMOX1 EXPRESSION Expression True +355 CDKN1A EXPRESSION Expression True +356 ALCAM EXPRESSION Expression True +357 STMN1 EXPRESSION Expression True +361 ERBB3 EXPRESSION Expression True +363 UGT1A EXPRESSION Expression True +365 ERBB4 EXPRESSION Expression True +366 SLFN11 EXPRESSION Expression True +372 CDKN1B EXPRESSION Expression True +373 AGR2 EXPRESSION Expression True +380 IGF1R EXPRESSION Expression True +381 EPHB4 EXPRESSION Expression True +383 TOP2A EXPRESSION Expression True +384 TOP1 EXPRESSION Expression True +386 HSPA5 EXPRESSION Expression True +389 TUBB3 EXPRESSION Expression True +392 CFLAR EXPRESSION Expression True +393 PROM1 EXPRESSION Expression True +394 FOXP3 EXPRESSION Expression True +398 DUSP6 EXPRESSION Expression True +400 HSPB1 EXPRESSION Expression True +401 NQO1 EXPRESSION Expression True +405 CXCR4 EXPRESSION Expression True +406 MAGEH1 EXPRESSION Expression True +410 CDX2 EXPRESSION Expression True +412 POU5F1 EXPRESSION Expression True +423 HLA-DRA EXPRESSION Expression True +429 KIT EXPRESSION Expression True +444 NEDD9 EXPRESSION Expression True +474 CIP2A EXPRESSION Expression True +476 MIR218-1 EXPRESSION Expression True +492 ECSCR EXPRESSION Expression True +493 ROBO4 EXPRESSION Expression True +537 RB1 EXPRESSION Expression True +546 ACTA1 EXPRESSION Expression True +624 MKI67 EXPRESSION Expression True +625 RAD23B EXPRESSION Expression True +651 AXL EXPRESSION Expression True +652 GAS6 EXPRESSION Expression True +660 HIF1A EXPRESSION Expression True +662 MLH1 EXPRESSION Expression True +670 MYCL EXPRESSION Expression True +671 HGF EXPRESSION Expression True +673 FGF2 EXPRESSION Expression True +700 KIF23 EXPRESSION Expression True +857 NTRK3 EXPRESSION Expression False +1258 PTPRF EXPRESSION Expression False +1262 MDM4 EXPRESSION Expression False +1284 DCC EXPRESSION Expression True +2163 CTLA4 EXPRESSION Expression False +2207 PDCD1LG2 EXPRESSION Expression False +2208 LAG3 EXPRESSION Expression False +2594 ASCL1 EXPRESSION Expression False +2984 CXCL10 EXPRESSION Expression False +3042 CDK6 EXPRESSION Expression True +3330 TCF19 EXPRESSION Expression False +1854 EGFR Ex19 del L858R Region Defined Variant True +2870 VHL Exon 1 (Frameshift) Other False +844 VHL Exon 1 Deletion Region Defined Variant True +2465 VHL Exon 1 del (151nt) Region Defined Variant False +845 VHL Exon 1-2 Deletion Region Defined Variant True +843 VHL Exon 1-3 Deletion Region Defined Variant True +4168 VHL Transcript Variant False +4169 VHL Transcript Variant False +106 PIK3CA Exon 10 Mutation Region Defined Variant True +1991 PIK3CA Exon 10 and Exon 21 Mutation Region Defined Variant True +3311 PIK3CA Exon 10 or Exon 21 Mutation Region Defined Variant True +66 KIT Exon 11 Mutation Region Defined Variant True +2643 KIT Exon 13 Mutation Region Defined Variant True +69 KIT Exon 14 Mutation Region Defined Variant True +2778 MET Exon 14 Mutation Region Defined Variant False +324 MET Exon 14 Skipping Mutation Region Defined Variant True +2650 BRAF Exon 15 Mutation Region Defined Variant True +4491 ERBB2 Exon 17 V659E Region Defined Variant False +2623 PDGFRA Exon 18 Mutation Region Defined Variant True +375 EGFR Exon 18 Overexpression Other True +2257 EGFR Exon 18 deletion Region Defined Variant False +133 EGFR Exon 19 Deletion Region Defined Variant True +4490 ERBB2 Exon 19 L755P Region Defined Variant False +1938 VHL Exon 2 Deletion Region Defined Variant True +75 KRAS Exon 2 Mutation Region Defined Variant True +1971 VHL Exon 2-3 Deletion Region Defined Variant False +4485 ERBB2 Exon 20 A775_G776ins YVMA Region Defined Variant False +4484 ERBB2 Exon 20 A775_G776insIVMA Region Defined Variant False +4483 ERBB2 Exon 20 A775_G776insYVMA Region Defined Variant False +4488 ERBB2 Exon 20 G776_V777>VCV Region Defined Variant False +4489 ERBB2 Exon 20 G776delinsVC Region Defined Variant False +4487 ERBB2 Exon 20 G778-779 insCPG Region Defined Variant False +4486 ERBB2 Exon 20 G778_P780dup Other False +726 EGFR Exon 20 Insertion Other True +2854 ERBB2 Exon 20 Insertion Other True +105 PIK3CA Exon 21 Mutation Region Defined Variant True +1939 VHL Exon 3 Deletion Region Defined Variant True +1973 VHL Exon 3 Deletion Region Defined Variant False +2047 CTNNB1 Exon 3 Deletion Region Defined Variant False +2892 CTNNB1 Exon 3 Mutation Region Defined Variant True +3749 VHL Exon 3 Variant Region Defined Variant False +4250 VHL Transcript Variant False +4245 VHL Transcript Variant False +252 EGFR Exon 4 Deletion Region Defined Variant True +350 SETBP1 Exon 4 Mutation Region Defined Variant True +550 ALK Exon 4-11 Deletion Region Defined Variant True +129 WT1 Exon 7 Mutation Region Defined Variant True +4492 ERBB2 Exon 8 S310F Region Defined Variant False +4493 ERBB2 Exon 8 S335C Region Defined Variant False +130 WT1 Exon 9 Mutation Region Defined Variant True +509 KIT Exon 9 Mutation Region Defined Variant True +3100 VHL Exon Deletion Region Defined Variant False +19 CCND1 Expression Expression True +210 PGR Expression Expression True +268 FGFR1 Expression Expression True +276 CD274 Expression Expression True +313 PTEN Expression Expression True +314 NRG1 Expression Expression True +315 AREG Expression Expression True +329 ERCC1 Expression Expression True +354 EGFR Expression Expression True +376 ZEB1 Expression Expression True +397 BRCA1 Expression Expression True +533 SMAD4 Expression Expression True +683 PAX8 Expression Expression True +2209 DLL3 Expression Expression False +2595 HDAC2 Expression Expression False +2914 ALK Expression Expression False +2966 MGMT Expression Expression False +2993 CDK5 Expression Expression False +3014 CSF1R Expression Expression False +3319 BTK Expression Expression False +3320 BLK Expression Expression False +3992 STAT1 Expression Expression False +4336 FLT3LG Expression Expression False +4421 TBX2 Expression Expression False +4422 TBXT Expression Expression False +4206 VHL Transcript Variant False +3984 VHL Transcript Variant False +3363 VHL Transcript Variant False +3295 VHL Transcript Variant False +2423 VHL Transcript Variant False +2558 VHL Transcript Variant False +3143 VHL Transcript Variant False +3129 VHL Transcript Variant False +2096 VHL Transcript Variant False +2542 VHL Transcript Variant False +2621 KIT F506_F508DUP Copy Number True +4083 VHL Transcript Variant False +4082 VHL Transcript Variant False +2271 VHL Transcript Variant False +3494 VHL Transcript Variant False +4081 VHL Transcript Variant False +3577 VHL Transcript Variant False +3157 VHL Transcript Variant True +2018 VHL Transcript Variant False +2158 VHL F76fs (c.222_225dup) Copy Number False +1912 VHL F76fs (c.223_224insT) Copy Number True +3632 VHL Transcript Variant False +1893 VHL Transcript Variant True +3105 VHL Transcript Variant False +2656 BRAF FAM131B::BRAF Fusion False +2987 BRAF FAM73A::BRAF Fusion False +2743 FGFR1 FGFR1OP2::FGFR1 Fusion True +4498 FGFR1 FGFR1OP::FGFR1 Fusion False +783 FGFR2 FGFR2::AHCYL1 Fusion True +782 FGFR2 FGFR2::BICC1 Fusion True +52 FGFR2 FGFR2::MGEA5 Fusion True +54 FGFR2 FGFR2::TACC3 Fusion True +53 FGFR3 FGFR3::BAIAP2L1 Fusion True +830 FGFR3 FGFR3::TACC3 Fusion True +574 PDGFRA FIP1L1::PDGFRA Fusion True +577 PDGFRA FIP1L1::PDGFRA T674I Fusion True +4468 ALK FN1::ALK Fusion False +2682 ABL1 FOXP1::ABL1 Fusion True +667 MEN1 FRAMESHIFT TRUNCATION Protein Consequence True +722 DDIT3 FUS::DDIT3 Fusion True +3149 RELA FUSION Fusion False +575 ROS1 FUSIONS Fusion False +428 MRE11 Frameshift Protein Consequence True +2812 MBD4 Frameshift Protein Consequence False +124 TSC1 Frameshift Truncation Protein Consequence True +419 NTRK1 Fusion Fusion True +499 ALK Fusion Fusion True +524 DUX4 Fusion Fusion True +567 PDGFRA Fusion Fusion True +568 PDGFRB Fusion Fusion True +569 FGFR1 Fusion Fusion True +1277 NTRK3 Fusion Fusion True +1687 RET Fusion Fusion True +1691 FGFR3 Fusion Fusion True +2202 FGFR2 Fusion Fusion True +2286 NRG1 Fusion Fusion True +2566 ABL1 Fusion Fusion False +2571 ABL2 Fusion Fusion True +2572 JAK2 Fusion Fusion False +2639 BRAF Fusion Fusion False +2640 NTRK2 Fusion Fusion True +2693 ROS1 Fusion Fusion True +2779 STAT6 Fusion Fusion False +2806 KMT2A Fusion Fusion False +2830 ETV1 Fusion Fusion False +3081 RAF1 Fusion Fusion False +3315 TP53 Fusion Fusion False +3957 RASGRF1 Fusion Fusion False +3637 VHL Transcript Variant False +2252 VHL Transcript Variant False +2266 VHL Transcript Variant False +2551 VHL Transcript Variant False +3085 VHL Transcript Variant False +4084 VHL Transcript Variant False +2073 VHL Transcript Variant False +4174 VHL Transcript Variant False +2455 VHL Transcript Variant True +2129 VHL Transcript Variant True +2153 VHL Transcript Variant False +76 KRAS G12 Protein Consequence True +92 NRAS G12 Protein Consequence True +77 KRAS G12/G13 Protein Consequence True +596 NRAS G12/G13 Protein Consequence True +2135 VHL Transcript Variant True +3099 VHL Transcript Variant False +80 KRAS G13 Protein Consequence True +4172 VHL Transcript Variant False +4211 VHL Transcript Variant False +2319 VHL Transcript Variant False +2320 VHL Transcript Variant False +1949 VHL Transcript Variant True +2721 TP53 G245 Protein Consequence False +2724 TP53 G266 Protein Consequence False +3736 VHL Transcript Variant False +2961 RUNX1 Transcript Variant False +3587 H3-3A G34 Protein Consequence False +3046 VHL Transcript Variant False +3742 KIT G3BP2::KIT Fusion False +2822 BRAF G469 Protein Consequence True +3469 NTRK1 G595R and G667S Protein Consequence True +2768 BRAF G596 Protein Consequence False +730 MLH1 G606FS*2 Protein Consequence True +718 EGFR G719 Protein Consequence True +1557 ERBB2 G776INSV_G/C Protein Consequence False +817 ERBB2 G778_P780DUP Copy Number True +3033 RET G810 Protein Consequence False +3263 VHL Transcript Variant False +2097 VHL Transcript Variant True +1812 VHL Transcript Variant False +3214 JAK2 GOLGA5::JAK2 Fusion True +2395 NTRK1 GON4L::NTRK1 Fusion True +2770 ROS1 GOPC::ROS1 Fusion True +4240 TYR GRCh37/hg19 11q14.3(chr11:88960991-88961138)x160 Copy Number False +3305 TNFRSF17 Gain Copy Number False +4424 TBXT Gain Copy Number False +2061 ACVR1 Gain-of-Function Other True +2172 MTOR Gain-of-Function Other False +1765 EGFR Gain-of-function Other True +2346 MLH1 Transcript Variant False +3766 PIK3CA H1047L or H1047R Protein Consequence True +4185 VHL Transcript Variant False +2540 VHL Transcript Variant False +2136 VHL Transcript Variant True +4093 VHL Transcript Variant False +2328 VHL Transcript Variant False +2581 NCOA2 HEY1::NCOA2 Fusion True +4405 ALK HIP1::ALK Fusion True +2969 HMGA2 HMGA2::LPP Fusion False +3597 DDR2 High expression Expression False +1965 VHL Transcript Variant False +527 ALK I1171 Protein Consequence True +2095 VHL Transcript Variant False +3136 VHL Transcript Variant False +3154 VHL Transcript Variant False +2487 VHL Transcript Variant False +271 ATR I774FS Protein Consequence True +3232 FLT3 I836 Protein Consequence False +765 MSH6 I891FS Protein Consequence True +151 BCL2 IGH::BCL2 Fusion True +2663 CRLF2 IGH::CRLF2 Fusion True +4309 FGFR3 IGHA1::FGFR3 Fusion False +2744 IKZF1 IKZF1 deletion and mutation Region Defined Variant True +2686 IL2RB IL2RB::MYH9 Fusion False +218 SMARCA4 INACTIVATING MUTATION Gene Function True +2238 BARD1 ISOFORM EXPRESSION Expression False +55 FLT3 ITD Rearrangements True +3220 FLT3 ITD N676D Rearrangements False +3209 FLT3 ITD & D835(V/Y/F/H) Rearrangements False +3211 FLT3 ITD & D839G Rearrangements False +3284 FLT3 ITD & L601F Rearrangements False +3636 FLT3 ITD & N841K Rearrangements False +3118 FLT3 ITD & TKD MUTATIONS Other False +3283 FLT3 ITD & Y597F Rearrangements False +3210 FLT3 ITD & Y842C Rearrangements False +3219 FLT3 ITD D651G Rearrangements False +3221 FLT3 ITD I687F Rearrangements False +2785 FLT3 ITD N676K Rearrangements False +3218 FLT3 ITD and co-mutations Rearrangements False +3208 FLT3 ITD&F691(I/L) Rearrangements False +788 CHEK2 IVS2+1G>A Other True +2674 RB1 IVS20, A-G, -2 Other False +2895 NUDT15 Inactivating Mutation Gene Function False +67 KIT Internal Duplication Copy Number True +2659 FGFR1 Internal Duplication Copy Number True +4150 BCOR Internal tandem duplication Copy Number False +4229 BCOR Internal tandem duplication (ITD) Other False +257 EZH2 Intron 6 Mutation Region Defined Variant True +2134 VHL Transcript Variant True +2311 VHL Transcript Variant False +2722 TP53 K132 Protein Consequence False +3354 VHL Transcript Variant False +4088 VHL Transcript Variant False +4089 VHL Transcript Variant False +279 NF2 K159fs Protein Consequence True +4100 VHL Transcript Variant False +1872 VHL K159fs (c.473dup) Copy Number True +2040 VHL Transcript Variant True +2988 PCNA K164R LOSS-OF-MODIFICATION Other False +2327 VHL Transcript Variant False +2140 VHL Transcript Variant True +2499 VHL Transcript Variant False +3476 H3-3A K27 Protein Consequence False +3010 ABL1 K356dup Copy Number False +3273 MSH3 K383fs Protein Consequence False +4177 PDGFRA K385 Protein Consequence False +1166 ATM K468FS Protein Consequence True +2765 BRAF K601 Protein Consequence False +508 PMS2 K706FS*19 Protein Consequence True +2964 RUNX1 K90fsX101 Protein Consequence False +3158 NTRK2 KANK1::NTRK2 Fusion True +4001 ALK KANK4::ALK Fusion True +618 BRAF KIAA1549::BRAF Fusion True +4300 EGFR KIF5B::EGFR Fusion False +2707 MET KIF5B::MET Fusion False +273 RET KIF5B::RET Fusion True +1689 RET KIF5B::RET G810A Fusion False +1688 RET KIF5B::RET V804L Fusion False +3552 KMT2A KMT2A::ABI1 Fusion False +3551 KMT2A KMT2A::AF10 Fusion False +3550 KMT2A KMT2A::AF6 Fusion False +432 KMT2A KMT2A::MLLT3 Fusion True +3117 KMT2A KMT2A::MLLT4 Fusion False +2210 ASNS KMT2E::ASNS Fusion False +3472 KRAS KRAS4A Other False +3471 KRAS KRAS4A underexpression Other False +413 ERBB2 Kinase Domain Mutation Region Defined Variant True +3294 VHL Transcript Variant False +2731 TP53 L114 Protein Consequence False +2312 VHL Transcript Variant False +2381 VHL Transcript Variant False +2313 VHL Transcript Variant False +1768 VHL Transcript Variant True +3172 VHL Transcript Variant False +1996 VHL Transcript Variant True +2557 VHL Transcript Variant False +3119 VHL Transcript Variant False +4087 VHL Transcript Variant False +3753 VHL Transcript Variant False +1960 VHL Transcript Variant True +3513 VHL Transcript Variant False +4236 VHL Transcript Variant False +1802 VHL Transcript Variant True +2324 VHL Transcript Variant False +4160 VHL Transcript Variant False +1783 VHL L158fs (c.471dupT) Copy Number True +3278 VHL Transcript Variant False +2459 VHL Transcript Variant True +3091 VHL Transcript Variant False +4092 VHL Transcript Variant False +4238 VHL Transcript Variant False +4199 VHL Transcript Variant False +4156 VHL Transcript Variant False +3480 VHL Transcript Variant False +4225 VHL Transcript Variant False +2735 TP53 L206 Protein Consequence False +1318 TP53 L3 Domain Mutation Region Defined Variant False +1677 FBXW7 L403FS*34 Protein Consequence False +541 PALB2 L531FS*30 Protein Consequence True +2766 BRAF L597 Protein Consequence False +2262 VHL Transcript Variant False +2087 VHL Transcript Variant False +2997 EGFR L718V and L718Q Protein Consequence False +1011 EGFR L747_P753>Q Rearrangements False +4221 AKT2 L78_Q79ins Rearrangements False +2506 VHL Transcript Variant False +1925 VHL Transcript Variant False +2305 VHL Transcript Variant False +1866 EGFR L861 Protein Consequence True +3164 VHL Transcript Variant False +3483 LGR5 LGR5FL Expression False +1278 NTRK1 LMNA::NTRK1 Fusion True +1282 NTRK1 LMNA::NTRK1 G595R and G667C Fusion True +3225 NTRK1 LMNA::NTRK1 e11-e10 Fusion True +3223 NTRK1 LMNA::NTRK1 e2-e10 Fusion True +3224 NTRK1 LMNA::NTRK1 e2-e11 Fusion True +302 PTCH1 LOH Genotypes Compound True +564 SMAD4 LOSS Gene Function True +809 MSH6 LOSS Gene Function True +3659 SMARCB1 LOSS OF NUCLEAR PROTEIN EXPRESSION Expression False +2596 LZTR1 LOSS-OF-FUNCTION Gene Function False +2755 FUBP1 LOSS-OF-FUNCTION Gene Function False +2968 HMGA2 LPP::HMGA2 Fusion False +3272 ABL1 LSM14A::ABL1 Fusion True +23 CCND3 Loss Gene Function True +214 PTEN Loss Gene Function True +370 MRE11 Loss Gene Function True +436 VHL Loss Gene Function True +485 STK11 Loss Gene Function True +554 CDKN2A Loss Gene Function True +555 CDKN2B Loss Gene Function True +672 SOX10 Loss Gene Function True +697 NF2 Loss Gene Function True +698 NF1 Loss Gene Function True +808 MSH2 Loss Gene Function True +853 NBN Loss Gene Function False +925 STK11 Loss Gene Function False +1876 CIC Loss Gene Function False +1879 ATXN1L Loss Gene Function False +1880 ATM Loss Gene Function False +2212 BAP1 Loss Gene Function False +2230 ASS1 Loss Gene Function True +2232 FLCN Loss Gene Function False +2234 KMT2D Loss Gene Function False +2365 TF Loss Gene Function False +2644 SMARCA4 Loss Gene Function True +2754 PRKN Loss Gene Function False +3202 SMARCB1 Loss Gene Function True +4310 KDM6A Loss Gene Function False +4452 TP53 Loss Gene Function True +125 TSC1 Loss-of-function Gene Function True +131 BRCA1 Loss-of-function Gene Function True +132 BRCA2 Loss-of-function Gene Function True +159 VHL Loss-of-function Gene Function True +167 KMT2D Loss-of-function Gene Function True +230 CHEK2 Loss-of-function Gene Function True +236 CDK12 Loss-of-function Gene Function True +534 FANCC Loss-of-function Gene Function True +601 NOTCH1 Loss-of-function Gene Function True +606 RB1 Loss-of-function Gene Function True +637 FBXW7 Loss-of-function Gene Function True +721 CYP2D6 Loss-of-function Gene Function True +819 PTPRB Loss-of-function Gene Function True +1293 ARID1A Loss-of-function Gene Function True +2171 TSC2 Loss-of-function Gene Function False +2219 BARD1 Loss-of-function Gene Function True +2235 RASA1 Loss-of-function Gene Function True +2236 ATM Loss-of-function Gene Function False +2415 SMAD4 Loss-of-function Gene Function False +2424 KMT2C Loss-of-function Gene Function False +2565 PTPN12 Loss-of-function Gene Function False +2705 PBRM1 Loss-of-function Gene Function False +3316 MEN1 Loss-of-function Gene Function False +4269 ATRX Loss-of-function Gene Function False +1247 BRCA2 M1R Other True +3720 VHL Transcript Variant False +2497 VHL Transcript Variant False +2269 VHL Transcript Variant False +2545 VHL Transcript Variant False +2473 VHL Transcript Variant False +1889 VHL M54fs (c.161dup) Copy Number True +638 RB1 M695FS*26 Protein Consequence True +2227 BRAF MACF1::BRAF Fusion True +3988 MAP3K8 MAP3K8 fusion Fusion False +3148 MEF2D MEF2D Rearrangement Rearrangements False +30 CSF1R MEF2D::CSF1R Fusion True +2894 MET MET::ATXN7L1 Fusion True +538 MLH1 METHYLATION Epigenetic Modification True +784 CDKN2B METHYLATION Epigenetic Modification True +3114 MN1 MN1::CXXC5 Fusion False +217 SMARCA4 MUTATION Region Defined Variant True +521 U2AF1 MUTATION Region Defined Variant True +595 SRSF2 MUTATION Region Defined Variant True +623 POT1 MUTATION Region Defined Variant True +644 PRDM1 MUTATION Region Defined Variant True +659 NF2 MUTATION Region Defined Variant False +664 CDH1 MUTATION Region Defined Variant True +665 RHOA MUTATION Region Defined Variant True +668 KMT2C MUTATION Region Defined Variant True +669 STAG2 MUTATION Region Defined Variant True +674 EIF1AX MUTATION Region Defined Variant True +2169 BTK MUTATION Region Defined Variant True +2170 PLCG2 MUTATION Region Defined Variant True +2652 H3-3A MUTATION Region Defined Variant True +2761 ZRSR2 MUTATION Region Defined Variant False +2773 RABL3 MUTATION Region Defined Variant False +3052 CD79B MUTATION Region Defined Variant False +3073 CARD11 MUTATION Region Defined Variant False +3138 NPM1 MUTATION Region Defined Variant False +2665 MYB MYB::GATA1 Fusion False +4327 MYB MYB::QKI Fusion False +29 CEBPA Mutation Region Defined Variant True +155 RUNX1 Mutation Region Defined Variant True +157 TET2 Mutation Region Defined Variant True +160 VHL Mutation Region Defined Variant True +161 PBRM1 Mutation Region Defined Variant True +163 EZH2 Mutation Region Defined Variant True +174 APC Mutation Region Defined Variant True +177 ASXL1 Mutation Region Defined Variant True +178 ATM Mutation Region Defined Variant True +183 BAP1 Mutation Region Defined Variant True +185 BRCA1 Mutation Region Defined Variant True +186 BRCA2 Mutation Region Defined Variant True +189 DNMT3A Mutation Region Defined Variant True +206 NOTCH1 Mutation Region Defined Variant True +208 NRAS Mutation Region Defined Variant True +215 SF3B1 Mutation Region Defined Variant True +216 SMAD4 Mutation Region Defined Variant True +222 TP53 Mutation Region Defined Variant True +275 HRAS Mutation Region Defined Variant True +277 MTOR Mutation Region Defined Variant True +281 FBXW7 Mutation Region Defined Variant True +297 RIT1 Mutation Region Defined Variant True +300 SMO Mutation Region Defined Variant True +301 PTCH1 Mutation Region Defined Variant True +310 ERBB4 Mutation Region Defined Variant True +311 PIK3CA Mutation Region Defined Variant True +323 MET Mutation Region Defined Variant True +327 PTPRD Mutation Region Defined Variant True +336 KRAS Mutation Region Defined Variant True +388 KIT Mutation Region Defined Variant True +399 BRAF Mutation Region Defined Variant True +442 EGFR Mutation Region Defined Variant True +505 GNAQ Mutation Region Defined Variant True +506 GNA11 Mutation Region Defined Variant True +510 PTEN Mutation Region Defined Variant True +511 FGFR2 Mutation Region Defined Variant True +512 ALK Mutation Region Defined Variant True +519 FLT3 Mutation Region Defined Variant True +560 CSF3R Mutation Region Defined Variant True +570 IDH2 Mutation Region Defined Variant True +587 NF1 Mutation Region Defined Variant True +600 AR Mutation Region Defined Variant True +633 PIK3R1 Mutation Region Defined Variant True +645 IDH1 Mutation Region Defined Variant True +663 BCOR Mutation Region Defined Variant True +666 ERBB2 Mutation Region Defined Variant True +713 CRBN Mutation Region Defined Variant True +715 STK11 Mutation Region Defined Variant True +797 POLE Mutation Region Defined Variant True +799 RB1 Mutation Region Defined Variant True +827 FGFR3 Mutation Region Defined Variant True +1690 RET Mutation Region Defined Variant False +2231 FLCN Mutation Region Defined Variant False +2233 BCL2 Mutation Region Defined Variant True +2237 KDM5C Mutation Region Defined Variant False +2388 CALR Mutation Region Defined Variant True +2567 ETV6 Mutation Region Defined Variant False +2641 FGFR1 Mutation Region Defined Variant False +2642 PTPN11 Mutation Region Defined Variant False +2668 FOXO3 Mutation Region Defined Variant False +2692 B2M Mutation Region Defined Variant False +2699 CBL Mutation Region Defined Variant False +2704 CDKN2A Mutation Region Defined Variant True +2749 NFE2L2 Mutation Region Defined Variant True +2759 PALB2 Mutation Region Defined Variant True +2760 MPL Mutation Region Defined Variant False +2764 CDK12 Mutation Region Defined Variant True +2898 NT5C2 Mutation Region Defined Variant True +2958 SDHB Mutation Region Defined Variant False +2983 ACVR1 Mutation Region Defined Variant True +3072 GATA2 Mutation Region Defined Variant False +3115 GATA1 Mutation Region Defined Variant False +3203 ATRX Mutation Region Defined Variant True +3274 PDGFRA Mutation Region Defined Variant True +4018 MS4A1 Mutation Region Defined Variant True +4437 PPP2R2A Mutation Region Defined Variant True +4438 RAD54L Mutation Region Defined Variant True +4439 BRIP1 Mutation Region Defined Variant True +4440 BARD1 Mutation Region Defined Variant True +4441 CHEK1 Mutation Region Defined Variant True +4442 FANCL Mutation Region Defined Variant False +4443 RAD51B Mutation Region Defined Variant True +4444 RAD51C Mutation Region Defined Variant False +4445 RAD51D Mutation Region Defined Variant True +4471 ARAF Mutation Region Defined Variant False +4503 RAF1 Mutation Region Defined Variant False +4504 MAP2K1 Mutation Region Defined Variant False +4505 MAP2K2 Mutation Region Defined Variant False +4506 GATA3 Mutation Region Defined Variant False +4507 GNAS Mutation Region Defined Variant False +3127 WT1 Mutations Region Defined Variant False +28 CEBPA N-TERMINAL FRAME SHIFT Protein Consequence True +1981 VHL Transcript Variant False +4271 VHL Transcript Variant False +2315 VHL Transcript Variant False +2272 VHL Transcript Variant False +1823 VHL Transcript Variant False +3186 VHL Transcript Variant False +2029 VHL Transcript Variant True +3493 VHL Transcript Variant False +3743 VHL Transcript Variant False +3759 VHL Transcript Variant False +3317 VHL Transcript Variant False +2253 VHL Transcript Variant False +4230 VHL Transcript Variant False +3655 VHL Transcript Variant False +4078 VHL Transcript Variant False +4159 VHL Transcript Variant False +2547 VHL Transcript Variant False +1581 EGFR N771>GY Rearrangements False +4201 VHL Transcript Variant False +2309 VHL Transcript Variant False +1320 ERBB2 NON-AMPLIFICATION Copy Number False +513 ALK NPM::ALK Fusion True +2883 BRAF NRF1::BRAF Fusion True +2762 NRG1 NRG1 FUSIONS Fusion False +3740 NTRK1 NTRK1 amplification Copy Number False +340 DKK1 NUCLEAR EXPRESSION Expression True +368 BIRC5 NUCLEAR EXPRESSION Expression True +391 IGF1R NUCLEAR EXPRESSION Expression True +438 PSMB8 NUCLEAR EXPRESSION Expression True +439 PBK NUCLEAR EXPRESSION Expression True +490 HSPH1 NUCLEAR EXPRESSION Expression True +494 PIM1 NUCLEAR EXPRESSION Expression True +364 ERBB4 NUCLEAR TRANSLOCATION Rearrangements True +3271 ABL1 NUP153::ABL1 Fusion True +2660 ABL1 NUP214::ABL1 Fusion True +3111 NUP98 NUP98::KDM5A Fusion False +2593 NUP98 NUP98::NSD1 Fusion True +2376 ABL1 Non-P-Loop Mutation Region Defined Variant True +2408 BRAF Non-V600 Region Defined Variant True +3297 VHL Null (11 kb 3' deletion) Gene Function False +2016 VHL Null (Complete deletion) Gene Function False +2182 VHL Null (Large deletion) Gene Function True +1947 VHL Null (Partial deletion of 4.6 Kb) Gene Function False +2082 VHL Null (Partial deletion of Exon 1) Other False +1951 VHL Null (Partial deletion of Exon 2) Other False +1952 VHL Null (Partial deletion of Exon 3) Other False +2083 VHL Null (Partial deletion of Exons 1 & 2) Other False +2036 VHL Null (Partial deletion of Exons 2 & 3) Other True +2103 VHL Null (Partial deletion) Gene Function False +1978 VHL Transcript Variant False +1979 VHL Transcript Variant False +4264 VHL Transcript Variant False +3361 VHL Null (del one VHL allele) Gene Function False +3180 VHL Null (deletion) Gene Function False +3188 VHL Null (large 3' deletion) Gene Function False +3262 VHL Null (point mutation codon 238) Gene Function False +3296 VHL Null (rearrangement) Other False +2974 JAK2 OFD1::JAK2 Fusion True +21 CCND2 OVEREXPRESSION Expression True +205 NCOA3 OVEREXPRESSION Expression True +296 RIT1 OVEREXPRESSION Expression True +305 SYK OVEREXPRESSION Expression True +345 SPHK1 OVEREXPRESSION Expression True +348 PBK OVEREXPRESSION Expression True +359 AR OVEREXPRESSION Expression True +378 PTP4A3 OVEREXPRESSION Expression True +396 JAK1 OVEREXPRESSION Expression True +434 HIF1A OVEREXPRESSION Expression True +440 PTTG1 OVEREXPRESSION Expression True +796 RRM2 OVEREXPRESSION Expression True +1299 MERTK OVEREXPRESSION Expression True +2362 PIK3CA OVEREXPRESSION Expression False +2419 NR2F2 OVEREXPRESSION Expression False +2586 PARP1 OVEREXPRESSION Expression True +2917 LYN OVEREXPRESSION Expression True +2981 WDR12 OVEREXPRESSION Expression False +2982 PLK1 OVEREXPRESSION Expression False +3112 PALB2 Oncogenic Mutations (loss of function alterations) Other False +20 CCND1 Overexpression Expression True +24 CCNE1 Overexpression Expression True +152 BCL2 Overexpression Expression True +156 IGF2 Overexpression Expression True +181 AURKA Overexpression Expression True +193 EGFR Overexpression Expression True +289 ERBB3 Overexpression Expression True +290 NT5E Overexpression Expression True +291 EZH2 Overexpression Expression True +292 MYD88 Overexpression Expression True +325 FGFR3 Overexpression Expression True +346 CASP8 Overexpression Expression True +347 TYMS Overexpression Expression True +377 TIMP1 Overexpression Expression True +408 ABCC10 Overexpression Expression True +435 EPAS1 Overexpression Expression True +472 ALDH1A2 Overexpression Expression True +481 DDX43 Overexpression Expression True +483 TBK1 Overexpression Expression True +486 HAVCR2 Overexpression Expression True +525 B4GALT1 Overexpression Expression True +529 SIRT1 Overexpression Expression True +539 PTPN11 Overexpression Expression True +547 RB1 Overexpression Expression True +578 BIRC5 Overexpression Expression True +597 RET Overexpression Expression True +602 CDK6 Overexpression Expression True +603 FLT3 Overexpression Expression True +607 ESR1 Overexpression Expression True +619 PTGS2 Overexpression Expression False +621 MET Overexpression Expression True +639 JUN Overexpression Expression True +640 FOS Overexpression Expression True +653 ETV4 Overexpression Expression True +693 SGK1 Overexpression Expression True +795 RRM1 Overexpression Expression True +858 CSF1 Overexpression Expression False +859 ROS1 Overexpression Expression False +860 NTRK1 Overexpression Expression True +866 MITF Overexpression Expression False +869 YAP1 Overexpression Expression False +875 ERBB2 Overexpression Expression True +1256 TERT Overexpression Expression False +1259 AEBP1 Overexpression Expression False +1273 CTAG1B Overexpression Expression True +1274 CTAG2 Overexpression Expression True +1279 BRD4 Overexpression Expression False +1301 AKT3 Overexpression Expression True +1303 MYC Overexpression Expression True +1306 TP53 Overexpression Expression True +1693 CHEK1 Overexpression Expression True +1877 ETV1 Overexpression Expression False +1878 ETV5 Overexpression Expression False +2167 FGFR4 Overexpression Expression False +2204 KDR Overexpression Expression False +2239 TPT1 Overexpression Expression False +2360 AKT1 Overexpression Expression True +2363 PIK3R2 Overexpression Expression True +2410 ERCC1 Overexpression Expression False +2417 FGFR2 Overexpression Expression False +2578 NOTCH3 Overexpression Expression False +2584 CDK9 Overexpression Expression False +2585 VEGFA Overexpression Expression False +2588 EPOR Overexpression Expression False +2635 ALK Overexpression Expression False +2636 CDK4 Overexpression Expression False +2679 WEE1 Overexpression Expression False +2717 PSMD4 Overexpression Expression False +2739 CRLF2 Overexpression Expression False +2784 FGF19 Overexpression Expression True +2808 WNT11 Overexpression Expression False +2904 FGFR1 Overexpression Expression False +2908 TACSTD2 Overexpression Expression False +2911 IL6 Overexpression Expression True +2915 ABCB1 Overexpression Expression True +2944 PDGFRA Overexpression Expression True +2955 STAT1 Overexpression Expression False +2970 VEGFC Overexpression Expression False +2973 PDGFRB Overexpression Expression True +2978 MIR21 Overexpression Expression False +2980 IL33 Overexpression Expression False +2985 CCN2 Overexpression Expression False +3006 FOXC2 Overexpression Expression False +3007 ZEB1 Overexpression Expression False +3008 CUL7 Overexpression Expression False +3139 MECOM Overexpression Expression False +3243 ACTL6A Overexpression Expression False +3249 MYCN Overexpression Expression False +3259 IGF1R Overexpression Expression True +3277 ZHX2 Overexpression Expression False +3279 HDAC2 Overexpression Expression False +3306 HDAC9 Overexpression Expression False +3307 FOXF1 Overexpression Expression False +3568 JAK2 Overexpression Expression False +3569 STAT5B Overexpression Expression False +3598 DDR2 Overexpression Expression False +3599 HDAC6 Overexpression Expression False +3646 HOXC10 Overexpression Expression False +3728 SLC29A1 Overexpression Expression True +3731 KIT Overexpression Expression False +3732 HSP90B1 Overexpression Expression False +3733 KRAS Overexpression Expression False +3734 COX2 Overexpression Expression False +3735 BRAF Overexpression Expression False +3746 CCNE2 Overexpression Expression False +4237 AURKB Overexpression Expression False +4297 FGFR1 Overexpression Expression False +3415 AR Overexpression of AR-V9 Expression False +3324 VEGFA Overexpression of VEGF121 Expression False +3325 VEGFA Overexpression of VEGF121 and VEGF110 Expression False +2375 ABL1 P-Loop Mutation Region Defined Variant True +3248 VHL Transcript Variant False +1682 ARID1A P1175FS*5 Protein Consequence True +4265 VHL Transcript Variant False +2495 VHL P138fs (c.410dup) Copy Number False +2526 VHL Transcript Variant False +2732 TP53 P153 Protein Consequence False +3162 VHL Transcript Variant False +4262 VHL Transcript Variant False +2879 VHL Transcript Variant False +2274 VHL Transcript Variant False +4263 VHL Transcript Variant False +3353 VHL Transcript Variant False +207 NOTCH1 P2514FS Protein Consequence True +4165 VHL Transcript Variant False +3087 VHL Transcript Variant False +2726 TP53 P278 Protein Consequence False +3491 VHL Transcript Variant False +4176 VHL Transcript Variant False +2350 CRLF2 P2RY8::CRLF2 Fusion False +2090 VHL Transcript Variant True +4233 VHL Transcript Variant False +756 MLH1 P536FS Protein Consequence True +4202 VHL Transcript Variant False +2474 VHL Transcript Variant False +3076 VHL Transcript Variant False +2303 VHL Transcript Variant False +2263 VHL Transcript Variant False +2121 VHL Transcript Variant False +2014 VHL Transcript Variant True +2546 VHL Transcript Variant False +4224 AKT1 P68-C77dup Copy Number False +4080 VHL Transcript Variant False +1955 VHL Transcript Variant True +4097 VHL Transcript Variant False +41 ERBB2 P780INS Rearrangements True +3298 VHL Transcript Variant False +3185 VHL Transcript Variant False +2496 VHL Transcript Variant False +1942 VHL Transcript Variant False +2306 VHL Transcript Variant False +3190 VHL Transcript Variant False +477 BRCA1 P968FS Protein Consequence True +2515 VHL Transcript Variant False +3199 VHL Transcript Variant False +3525 ABL2 PAG1::ABL2 Fusion False +286 BRAF PAPSS1::BRAF Fusion True +2582 FOXO1 PAX3::FOXO1 Fusion True +2861 JAK2 PAX5::JAK2 Fusion True +2583 FOXO1 PAX7::FOXO1 Fusion True +209 PAX8 PAX8::PPARG Fusion True +571 JAK2 PCM1::JAK2 Fusion True +2289 NTRK1 PDE4DIP::NTRK1 Fusion True +387 EIF4EBP1 PHOSPHORYLATION Epigenetic Modification True +395 RPS6 PHOSPHORYLATION Epigenetic Modification True +632 RB1 PHOSPHORYLATION Epigenetic Modification True +108 PML PML::RARA Fusion True +3025 PML PML::RARA A216T Fusion False +462 PML PML::RARA A216V Fusion True +463 PML PML::RARA L218P Fusion True +3024 PML PML::RARA S214L Fusion False +2848 JAK2 PPFIBP1::JAK2 Fusion True +617 BRAF PPFIBP2::BRAF Fusion True +3235 PRKAR1A PRKAR1A LOH, allelic imbalance 17q Genotypes Compound False +22 CCND2 PROMOTER DEMETHYLATION Epigenetic Modification True +2254 DBI PROMOTER DEMETHYLATION Epigenetic Modification False +711 KLLN PROMOTER METHYLATION Epigenetic Modification True +2916 PRPS1 PRPS1 MUTATION Region Defined Variant True +2683 PTK2B PTK2B::KDM6A Fusion False +2684 PTK2B PTK2B::STAG2 Fusion False +4189 VHL Transcript Variant False +2184 VHL Partial deletion of 0.7 Kb Region Defined Variant False +4200 VHL Partial deletion of 0.8 kb Region Defined Variant False +2185 VHL Partial deletion of 1 Kb Region Defined Variant False +2186 VHL Partial deletion of 1.2 Kb Region Defined Variant False +2187 VHL Partial deletion of 1.5 Kb Region Defined Variant False +3999 VHL Partial deletion of 10 Kb Region Defined Variant False +2188 VHL Partial deletion of 11 Kb Region Defined Variant False +2189 VHL Partial deletion of 12 Kb Region Defined Variant False +3095 VHL Partial deletion of 2 Kb Region Defined Variant False +2191 VHL Partial deletion of 3 Kb Region Defined Variant False +2190 VHL Partial deletion of 3.5 Kb Region Defined Variant False +2492 VHL Partial deletion of 4 Kb Region Defined Variant False +2193 VHL Partial deletion of 7 Kb Region Defined Variant False +2192 VHL Partial deletion of 7.5 Kb Region Defined Variant False +2194 VHL Partial deletion of 8.2 Kb Region Defined Variant False +3466 NTRK1 Point Mutations Other False +3467 NTRK3 Point Mutations Other False +27 CDKN2A Promoter Hypermethylation Epigenetic Modification True +333 PTPRT Promoter Hypermethylation Epigenetic Modification True +374 NAPRT Promoter Hypermethylation Epigenetic Modification True +85 MGMT Promoter Methylation Epigenetic Modification True +220 TERT Promoter Mutation Region Defined Variant True +2443 VHL Transcript Variant False +2267 VHL Transcript Variant False +2321 VHL Transcript Variant False +2155 VHL Transcript Variant False +2525 VHL Transcript Variant False +127 U2AF1 Q157P/R Protein Consequence True +4212 VHL Transcript Variant False +4094 VHL Transcript Variant False +2383 VHL Transcript Variant False +3657 VHL Transcript Variant False +507 GNAQ Q209 Protein Consequence True +558 GNA11 Q209 Protein Consequence True +4435 BAP1 Q267fs Protein Consequence False +744 MLH1 Q426FS Protein Consequence True +3326 FLT3 Q575Δ Other False +94 NRAS Q61 Protein Consequence True +203 KRAS Q61 Protein Consequence True +2570 HRAS Q61 Protein Consequence True +1105 KRAS Q61FS Protein Consequence False +2002 VHL Transcript Variant False +2444 VHL Transcript Variant False +2131 VHL Transcript Variant True +3145 VHL Transcript Variant False +4110 VHL Transcript Variant False +2251 VHL Transcript Variant False +4000 RAF1 QKI-RAF1 Fusion True +3176 VHL Transcript Variant False +4227 VHL Transcript Variant False +3029 BCL2 R107_R110dup Copy Number False +3132 VHL Transcript Variant False +4085 VHL Transcript Variant False +2021 VHL R108dup (c.322_324dup) Copy Number True +3633 VHL Transcript Variant False +3656 VHL Transcript Variant False +2537 VHL Transcript Variant False +2552 VHL Transcript Variant False +2996 ARID2 Transcript Variant False +58 IDH1 R132 Protein Consequence True +804 RUNX1 R135FSX177 Protein Consequence True +62 IDH2 R140 Protein Consequence True +4096 VHL Transcript Variant False +2273 VHL Transcript Variant False +3103 VHL Transcript Variant False +4167 VHL Transcript Variant False +4166 VHL Transcript Variant False +3121 VHL Transcript Variant False +4180 VHL Transcript Variant False +4210 VHL Transcript Variant False +4239 VHL Transcript Variant False +2486 VHL Transcript Variant False +1779 VHL Transcript Variant False +199 IDH2 R172 Protein Consequence True +3187 VHL Transcript Variant False +3355 VHL Transcript Variant False +4266 VHL Transcript Variant False +3191 VHL Transcript Variant False +2181 VHL Transcript Variant True +3044 VHL Transcript Variant False +3192 VHL Transcript Variant False +4190 VHL Transcript Variant False +4208 VHL Transcript Variant False +876 GNAS R201 Protein Consequence True +4095 VHL Transcript Variant False +3658 VHL Transcript Variant False +2723 TP53 R248 Protein Consequence False +119 TP53 R249 Protein Consequence True +2725 TP53 R273 Protein Consequence False +2965 RUNX1 Transcript Variant False +3134 SDHA Transcript Variant False +2597 DICER1 R392fs and E1813D Protein Consequence False +2959 CHEK2 Transcript Variant True +1964 VHL Transcript Variant True +735 MLH1 R687FS Protein Consequence True +2510 VHL Transcript Variant False +4079 VHL Transcript Variant False +1948 VHL Transcript Variant True +1165 ATM R777FS Protein Consequence False +4204 VHL Transcript Variant False +2448 VHL Transcript Variant True +3013 VHL Transcript Variant False +2264 VHL Transcript Variant True +3411 TEK R849W and R1108* Protein Consequence False +32 DNMT3A R882 Protein Consequence True +3268 ABL1 RANBP2::ABL1 Fusion True +514 ALK RANBP2::ALK Fusion True +3116 RBM15 RBM15::MKL1 Fusion False +3207 MET RBPMS::MET Fusion False +2681 ABL1 RCSD1::ABL1 Fusion True +2891 RCSD1 RCSD1::ABL1 Fusion False +3526 ABL2 RCSD1::ABL2 Fusion False +3527 CSF1R RCSD1::ABL2 Fusion False +2865 JAK2 RFX3::JAK2 Fusion True +332 FNTB RS11623866 Other True +338 MGMT RS16906252 Other True +643 CBLB RS2305035 Other True +421 TERT RS2736100 Other True +699 SH2B3 RS3184504 Other True +779 TYMS RS34743033 Other True +642 MDM2 RS34886328 Other True +482 KIT RS3733542 Other True +641 CDKN2A RS3814960 Other True +331 WEE1 RS3910384 Other True +777 SLCO1B1 RS4149056 Other True +445 ETS2 RS461155 Other True +548 PPP1R15A RS557806 Other True +254 KRAS RS61764370 Other True +740 DPYD RS67376798 HOMOZYGOSITY Other True +255 ERCC5 RS751402 Other True +3126 RUNX1 RUNX1::RUNX1T1 Fusion False +1863 EGFR Rare Exon 18-21 Mutation Region Defined Variant True +2334 EGFR Rare Mutation Other True +3222 PIK3CA Rare Mutation Other True +269 ROS1 Rearrangement Rearrangements True +2439 VHL Rearrangement Rearrangements True +3141 KMT2A Rearrangement Rearrangements False +4003 PDGFB Rearrangement Rearrangements False +4338 CRLF2 Rearrangement Rearrangements False +3747 VHL Transcript Variant False +4171 VHL Transcript Variant False +3080 VHL S139fs Protein Consequence False +2316 VHL Transcript Variant False +616 B2M S14FS Protein Consequence True +4154 VHL Transcript Variant False +2856 ROS1 S1986Y/F Protein Consequence False +138 NOTCH1 S2275FS Protein Consequence True +497 ERBB2 S310F/Y Protein Consequence True +128 U2AF1 S34Y/F Protein Consequence True +4076 VHL Transcript Variant False +4231 VHL Transcript Variant False +3257 AKT1 S473 Phosphorylation Epigenetic Modification True +3329 FLT3 S574Δ Other False +4099 VHL Transcript Variant False +2535 VHL Transcript Variant False +1676 FBXW7 S668FS*39 Protein Consequence False +720 EGFR S720 Protein Consequence True +3015 VHL Transcript Variant False +3704 VHL Transcript Variant False +2462 VHL Transcript Variant False +1511 EGFR S768_D770dup Copy Number True +4109 VHL Transcript Variant False +4184 VHL Transcript Variant False +451 ABCB1 S893A/T Protein Consequence True +4253 NTRK1 SCP2::NTRK1 Fusion False +2179 NRG1 SDC4::NRG1 Fusion True +4251 EGFR SEC61G::EGFR Fusion False +416 ERBB2 SERUM LEVELS Expression True +487 MMP2 SERUM LEVELS Expression True +488 MMP9 SERUM LEVELS Expression True +3287 ABL1 SFPQ::ABL1 Fusion True +411 STAT3 SH2 DOMAIN MUTATION Region Defined Variant True +3986 SH3PXD2A SH3PXD2A::HTRA1 Fusion False +2166 NRG1 SLC3A2::NRG1 Fusion True +2975 JAK2 SMU1::JAK2 Fusion True +536 SULT1E1 SNP Region Defined Variant False +495 MDM2 SNP309 Protein Consequence True +2976 JAK2 SNX29::JAK2 Fusion True +2678 ABL1 SNX2::ABL1 Fusion True +478 AR SPLICE VARIANT 7 Other False +800 NTRK1 SQSTM1::NTRK1 Fusion True +448 SSX1 SS18::SSX1 Fusion True +449 SSX2 SS18::SSX2 Fusion True +450 SSX4 SS18::SSX4 Fusion True +3566 CSF1R SSBP2::CSF1R Fusion False +2661 JAK2 SSBP2::JAK2 Fusion True +2849 JAK2 STRN3::JAK2 Fusion True +2218 ALK STRN::ALK Fusion True +2287 NTRK2 STRN::NTRK2 Fusion True +3108 VHL Single Allele Deletion Genotypes Compound False +4425 SMARCB1 Single nucleotide variant Region Defined Variant False +2518 VHL Transcript Variant False +4162 VHL Transcript Variant False +4226 VHL Transcript Variant False +3107 VHL Transcript Variant False +4086 VHL Transcript Variant False +4254 VHL Transcript Variant False +4255 VHL Transcript Variant False +4256 VHL Transcript Variant False +4257 VHL Transcript Variant False +4258 VHL Transcript Variant False +4259 VHL Transcript Variant False +4243 VHL Transcript Variant False +3436 VHL Transcript Variant False +2457 VHL Transcript Variant False +3370 VHL Transcript Variant False +3150 VHL Transcript Variant False +2471 VHL Transcript Variant False +4235 VHL Transcript Variant False +1954 VHL Transcript Variant False +3409 TEK T1105N and T1106N Protein Consequence False +4389 ALK T1151dup Copy Number True +4205 VHL Transcript Variant False +3479 VHL Transcript Variant False +2314 VHL Transcript Variant False +3738 VHL Transcript Variant False +2556 VHL Transcript Variant False +810 RUNX1 T148HFSX9 Protein Consequence True +2091 VHL Transcript Variant True +2092 VHL Transcript Variant True +2094 VHL Transcript Variant False +491 HSPH1 T17 DELETION Region Defined Variant True +2733 TP53 T170 Protein Consequence False +385 PRKAA2 T172 PHOSPHORYLATION Epigenetic Modification True +2142 VHL Transcript Variant True +1298 BRAF T599dup Copy Number False +3517 ZNF384 TAF15::ZNF384 Fusion False +3359 CSF1R TBL1XR1::CSF1R Fusion True +2862 JAK2 TERF2::JAK2 Fusion True +3730 TFE3 TFE3 fusion Fusion False +4074 TFEB TFEB amplification Copy Number False +576 ROS1 TFG::ROS1 Fusion True +2669 TGFBR3 TGFBR3 Protein Consequence False +56 FLT3 TKD MUTATION Gene Function True +2371 ABL1 TKD MUTATION Gene Function True +3128 TLX3 TLX3::BCL11B Fusion False +195 ERG TMPRSS2::ERG Fusion True +707 TMPRSS2 TMPRSS2::ERG Fusion False +3473 TNC TNC-L Expression False +774 PDGFRA TNKS2::PDGFRA Fusion True +3486 TOP2A TOP2A/90 Other False +2992 NTRK1 TPM3::NTRK1 Fusion True +4469 ALK TPM4::ALK Fusion False +2850 JAK2 TPR::JAK2 Fusion True +3465 NTRK1 TPR::NTRK1 Fusion False +287 BRAF TRIM24::BRAF Fusion True +4499 FGFR1 TRIM24::FGFR1 Fusion False +2393 NTRK1 TRIM63::NTRK1 Fusion True +739 FOS TRUNCATING FUSION Fusion True +590 BIRC3 TRUNCATING MUTATION Protein Consequence True +708 BRCA2 TRUNCATING MUTATION Protein Consequence True +3110 CREBBP TRUNCATING MUTATIONS AND DELETERIOUS SUBSTITUTIONS Protein Consequence False +4432 SNCAIP Tandem duplication Copy Number False +4026 FGFR2 Translocation Rearrangements False +4027 FGFR3 Translocation Rearrangements False +4428 MYC Translocation Rearrangements False +4429 BCL2 Translocation Rearrangements False +4430 BCL6 Translocation Rearrangements False +4500 FGFR1 Translocation Rearrangements False +223 TP53 Truncating Mutation Protein Consequence True +729 UGT1A1 UGT1A1*28 Genotypes Easy True +732 UGT1A1 UGT1A1*60 Genotypes Easy True +417 THBS2 UNDEREXPRESSION Expression True +441 LEPR UNDEREXPRESSION Expression True +446 KRT18 UNDEREXPRESSION Expression True +498 MIR218-1 UNDEREXPRESSION Expression True +2418 SPRY2 UNDEREXPRESSION Expression False +2863 JAK2 USP25::JAK2 Fusion True +179 ATM Underexpression Expression True +282 SMAD4 Underexpression Expression True +304 STK11 Underexpression Expression True +349 SMARCA4 Underexpression Expression True +382 TYMS Underexpression Expression True +403 BRCA1 Underexpression Expression True +422 STAG2 Underexpression Expression True +473 ALDH1A2 Underexpression Expression True +475 CIP2A Underexpression Expression True +648 ATRX Underexpression Expression True +654 STAG3 Underexpression Expression True +695 SMARCB1 Underexpression Expression True +867 MTAP Underexpression Expression True +868 VPS37A Underexpression Expression True +1255 MGMT Underexpression Expression True +1257 RRM1 Underexpression Expression True +2108 ARID1A Underexpression Expression True +2164 CX3CL1 Underexpression Expression False +2384 PBLD Underexpression Expression False +2386 ERRFI1 Underexpression Expression False +2392 PTPN6 Underexpression Expression False +2409 ERCC1 Underexpression Expression True +2412 FGFR2 Underexpression Expression False +2718 CCNE1 Underexpression Expression False +3459 AR V1 expression Expression False +2539 VHL Transcript Variant False +1167 ATM V1268FS Protein Consequence False +2086 VHL Transcript Variant False +4246 VHL Transcript Variant False +3366 VHL Transcript Variant False +4198 VHL Transcript Variant False +2046 VHL Transcript Variant True +3985 VHL Transcript Variant False +2477 VHL Transcript Variant False +3748 VHL Transcript Variant False +4091 VHL Transcript Variant False +4279 VHL Transcript Variant False +3089 VHL Transcript Variant False +3362 VHL Transcript Variant False +2325 VHL Transcript Variant False +3086 VHL Transcript Variant False +1977 VHL Transcript Variant True +750 MLH1 V213FS Protein Consequence True +137 NOTCH1 V2444FS Protein Consequence True +762 MSH2 V273FS Protein Consequence True +605 PTEN V317FS Protein Consequence True +1316 KIT V559 Protein Consequence False +3461 AR V567es expression Expression False +17 BRAF V600 Protein Consequence True +2820 BRAF V600_K601>E Rearrangements True +2821 BRAF V600_S602>DT Rearrangements False +3184 VHL Transcript Variant True +2509 VHL Transcript Variant False +3189 VHL Transcript Variant False +3261 VHL Transcript Variant False +2447 VHL Transcript Variant True +2099 VHL Transcript Variant True +362 AR V7 EXPRESSION Expression True +2445 VHL Transcript Variant False +4281 VHL Transcript Variant False +1310 ERBB2 V773 Protein Consequence False +2548 VHL Transcript Variant False +4179 VHL Transcript Variant False +3741 VHL Transcript Variant False +2159 AR V9 EXPRESSION Expression False +3729 TFE3 VCF::TFE3 Fusion False +3701 NTRK2 VCL::NTRK2 Fusion True +3303 CHD7 VCV000625197, Translocation (t(8;X)(q12.2;p22.13)), CHD7–BEND2 fusion Other False +3321 VEGFA VEGF165b Overexpression Expression False +312 EGFR VIII Gene Function True +4242 EGFR VOPP1::EGFR Fusion False +2470 VHL Transcript Variant False +3142 VHL Transcript Variant False +3715 VHL Transcript Variant False +2027 VHL W117fs (c.349dup) Copy Number True +3634 VHL Transcript Variant False +2728 TP53 W146 Protein Consequence False +87 NPM1 W288FS Protein Consequence True +176 AR W742 Protein Consequence True +2299 VHL W88fs (c.261dup) Copy Number True +2228 BRAF WASFL::BRAF Fusion True +426 BRAF WILD TYPE Genotypes Easy True +2366 PTEN WILD TYPE Genotypes Easy False +2651 KIT WILDTYPE Genotypes Easy True +742 WWTR1 WWTR1::CAMTA1 Fusion True +369 TP53 Wildtype Genotypes Easy True +2174 EGFR Wildtype Genotypes Easy True +2590 PIK3CA Wildtype Genotypes Easy True +3200 KRAS Wildtype Genotypes Easy True +4465 NRAS Wildtype Genotypes Easy False +390 EGFR Y1092 PHOSPHORYLATION Epigenetic Modification True +3739 VHL Transcript Variant False +245 NF2 Y177fs Protein Consequence True +2720 TP53 Y205 Protein Consequence False +3327 FLT3 Y572Δ Other False +165 EZH2 Y646 Protein Consequence True +3055 FLT3 Y693 Protein Consequence False +1672 EGFR Y69FS*11 Protein Consequence False +414 ERBB2 Y772_A775DUP Copy Number True +3410 TEK Y897C and R915C Protein Consequence False +3352 VHL Transcript Variant False +2450 VHL Transcript Variant False +3578 ABL2 ZC3HAV1::ABL2 Fusion False +657 BRAF ZKSCAN1::BRAF Fusion True +3269 ABL1 ZMIZ1::ABL1 Fusion True +4496 FGFR1 ZMYM2::FGFR1 Fusion False +466 FGFR1 ZNF198::FGFR1 Fusion True +2864 JAK2 ZNF274::JAK2 Fusion True +2977 JAK2 ZNF430::JAK2 Fusion True +3481 ESR2 alternative transcripts Other False +3477 ESR2 beta-2 and beta-5 Other False +4466 TERT Transcript Variant False +3021 VHL Transcript Variant False +3034 VHL Transcript Variant False +2634 VHL Transcript Variant False +3174 VHL Transcript Variant False +2633 VHL Transcript Variant False +3035 VHL Transcript Variant False +2373 VHL Transcript Variant True +3727 FLCN Transcript Variant True +3002 NF2 Transcript Variant True +3267 CBL Transcript Variant False +2884 CDKN2A Transcript Variant True +3404 PTEN Transcript Variant False +2374 VHL Transcript Variant False +4151 VHL Transcript Variant False +4228 VHL Transcript Variant False +4213 VHL Transcript Variant False +4209 VHL Transcript Variant False +3041 VHL Transcript Variant False +4178 VHL Transcript Variant False +2435 VHL Transcript Variant True +4197 VHL Transcript Variant False +4152 VHL Transcript Variant False +3088 VHL Transcript Variant False +3365 VHL Transcript Variant False +3159 VHL Transcript Variant False +4173 VHL Transcript Variant False +2507 VHL Transcript Variant False +4157 VHL Transcript Variant False +3047 VHL Transcript Variant False +3039 VHL Transcript Variant False +3050 ATM Transcript Variant True +3051 ATM Transcript Variant True +2433 VHL Transcript Variant False +3049 ATM Transcript Variant True +3101 VHL Transcript Variant False +4191 VHL Transcript Variant False +2431 VHL Transcript Variant True +3511 CD19 delta-ex2, delta-ex5-6 Other False +3487 BRCA1 delta11q Other False +3482 LGR5 delta5 Other False +2349 IL7R exon 6 mutations Region Defined Variant False +3752 SSTR5 expression Expression True +4416 EZH2 expression Expression True +4406 EGFR fusion Fusion False +2807 BRCA1 gBRCAm Other False +2226 BRAF intron 10 rearrangement Rearrangements True +2225 BRAF intron 9 rearrangement Rearrangements True +2814 DRD5 low expression Expression False +3323 VEGFA low ratio of VEGF165b/VEGFtotal Expression False +2845 HOXD8 mutation Region Defined Variant False +4436 CHEK2 mutation Region Defined Variant True +4463 TSC1 mutation Region Defined Variant False +4464 TSC2 mutation Region Defined Variant False +3322 VEGFA overexpression of VEGF-Axxxa Expression False +2411 SDHB p.193_196dupSTSC (c.577_588dupAGCACCAGCTGC) Copy Number True +4247 VHL Transcript Variant False +3057 GATA1 p.Ser51Alafs*86 Protein Consequence False +272 CDKN2A p16 Expression Expression True +3512 BRAF p61BRAF(V600E) Genotypes Easy False +3313 CDKN1A rs1059234 Other True +2787 PRNCR1 rs1456315 Other False +256 KIT rs17084733 Other True +2671 CDKN1A rs1801270 Other True +3314 CDKN1A rs1801270 and rs1059234 Other False +705 GADD45A rs681673 Other True +3703 GALNT14 rs9679162 Other False +4284 VHL t(1;3)(p36.3;p25) Rearrangements False +2429 VHL t(1;3)(q32;q13.3) Rearrangements False +2876 VHL t(2;3)(q35;q21) Rearrangements False +3265 VHL t(3;12)(q13.13;q24.23) Rearrangements False +4009 VHL t(3;12)(q13.2;q24.1) Rearrangements False +3524 MECOM t(3;21)(q26.2;q22) Rearrangements False +3264 VHL t(3;6)(p12.3;q24.3) Rearrangements False +4008 VHL t(3;6)(p13;q25.1) Rearrangements False +3351 VHL t(3;8)(p13;q24.1) Rearrangements False +3478 ESR2 underexpression beta-1 Other False +3508 CD274 v242 Protein Consequence False +2422 NTRK3 ~DEPRECATED-ETV6-NTRK3 Other False diff --git a/analysis/civic/should_be_able_to_normalize_genomic_variant_queries.csv b/analysis/civic/should_be_able_to_normalize_genomic_variant_queries.csv new file mode 100644 index 0000000..b44d190 --- /dev/null +++ b/analysis/civic/should_be_able_to_normalize_genomic_variant_queries.csv @@ -0,0 +1,426 @@ +variant_id hgvs_g variant_accepted +2489 NC_000003.11:g.10191648_10191649insC True +1988 NC_000003.11:g.10191649A>T True +2488 3-10191647-T-G True +1986 NC_000003.11:g.10191648G>T True +1987 NC_000003.11:g.10191649A>G True +2152 NC_000003.11:g.10191719C>A True +2024 3-10191656-C-G True +2028 NC_000003.11:g.10188221_10188222delinsAT True +3194 3-10188222-C-T False +820 NC_000003.11:g.10188302G>T True +1744 NC_000003.11:g.10188302G>A True +2042 NC_000003.11:g.10188302delG True +3173 NC_000003.11:g.10183681C>G False +771 NC_000003.11:g.10183695_10183696insG True +793 NC_000003.11:g.10183695_10183696insA True +1785 NC_000003.11:g.10183697_10183698insA True +2528 NC_000003.11:g.10191493C>A False +1773 NC_000003.11:g.10191492G>T True +1772 NC_000003.11:g.10191491T>C True +1774 NC_000003.11:g.10191493C>G True +1824 NC_000003.11:g.10191492G>A True +2035 NC_000003.11:g.10191490del True +3096 NC_000003.12:g.10142077_10142078insTCT True +2123 NC_000003.11:g.10183760_10183762del False +1813 NC_000003.11:g.10188219A>G True +2154 NC_000003.11:g.10188218G>C False +2446 NC_000003.11:g.10188218delG False +3133 3-10188218-G-A False +2554 NC_000003.11:g.10188234A>G False +2533 NC_000003.11:g.10188233G>A False +2053 NC_000003.11:g.10188233G>T False +3040 3-10188286-C-T False +3123 NC_000003.11:g.10191542G>A False +2579 NC_000007.13:g.50450370del False +2141 NC_000003.11:g.10191596del True +2105 NC_000003.11:g.10191596G>A False +2126 NC_000003.11:g.10191599_10191600del False +2449 NC_000003.11:g.10183806A>G True +2514 3-10183806-A-CC False +1694 NC_000003.11:g.10183567G>C False +1884 NC_000003.11:g.10188257G>T False +2524 NC_000003.12:g.10146575_10146601del False +2245 NC_000003.11:g.10191485G>T False +1919 NC_000003.11:g.10191486_10191487delAG True +2502 NC_000003.11:g.10191486A>T False +2098 NC_000003.12:g.10149800del True +2527 NC_000003.11:g.10191487delG False +1976 NC_000003.11:g.10191524G>T False +1777 NC_000003.11:g.10191563G>T True +1778 NC_000003.11:g.10191563G>A True +1829 NC_000003.11:g.10191565_10191567del False +1869 NC_000003.11:g.10191572del True +1733 NC_000003.11:g.10183667G>T True +2466 NC_000003.11:g.10183685G>T False +1734 NC_000003.11:g.10183685G>A True +1736 NC_000003.11:g.10183694G>T True +794 NC_000003.11:g.10183696G>A True +764 NC_000003.11:g.10183694_10183695del True +766 NC_000003.11:g.10183694del True +1834 NC_000003.11:g.10183739G>T True +1956 NC_000003.11:g.10183739G>A True +1794 NC_000003.11:g.10183811G>T True +2127 NC_000003.11:g.10183810del True +2173 NC_000003.11:g.10183811G>A False +2475 NC_000003.11:g.10188212T>C False +1743 NC_000003.11:g.10188214C>G True +2119 NC_000003.11:g.10188213T>C False +1945 NC_000003.11:g.10188211_10188212del False +1814 NC_000003.11:g.10188264T>G True +1801 NC_000003.11:g.10188264T>C True +1749 NC_000003.11:g.10183757T>A False +2107 NC_000003.11:g.10183759C>G False +1835 NC_000003.11:g.10183758T>C True +2088 NC_000003.11:g.10183758_10183760del True +1926 NC_000003.11:g.10183758_10183760delTCT False +2294 NC_000003.11:g.10183804C>G True +2293 NC_000003.11:g.10183843C>G True +2043 NC_000003.11:g.10183842G>C True +2428 NC_000003.11:g.10183842G>T True +1797 NC_000003.11:g.10183871G>T True +1857 NC_000003.11:g.10183871G>C True +2026 NC_000003.11:g.10183871G>A True +2491 NC_000003.11:g.10188198G>T False +2555 NC_000003.11:g.10188238delG False +1850 NC_000003.11:g.10188287G>T True +2290 3-10188288-G-A True +2059 NC_000003.11:g.10188287G>A False +3197 3-10188287-G-C False +3247 NC_000003.12:g.10146602_10146612del True +2560 NC_000003.11:g.10188288delG False +1737 NC_000003.11:g.10183645del False +2008 NC_000003.11:g.10183808G>T True +1858 NC_000003.11:g.10183809G>A False +1920 NC_000003.11:g.10183808G>C True +1859 NC_000003.11:g.10183808G>A True +2009 NC_000003.11:g.10183809G>T True +2463 NC_000003.11:g.10183860A>C False +2516 NC_000003.11:g.10183860del False +2520 NC_000003.11:g.10188200delC False +1885 NC_000003.11:g.10188201A>C True +1742 NC_000003.11:g.10188202C>A True +1957 NC_000003.11:g.10188202C>G True +2000 NC_000003.11:g.10188201A>G True +1921 NC_000003.11:g.10188200C>T True +2057 NC_000003.11:g.10188201del True +2060 NC_000003.11:g.10188231A>C False +3122 NC_000003.11:g.10188230C>T False +2425 NC_000003.11:g.10191578C>G False +1958 NC_000003.11:g.10191578del True +1922 NC_000003.11:g.10183857del False +2291 NC_000003.11:g.10188297T>C False +2038 NC_000003.11:g.10188296A>G False +2150 NC_000003.11:g.10188308A>T True +2030 NC_000003.11:g.10188310C>G True +2476 3-10188309-T-A False +2250 NC_000003.11:g.10188309T>G False +1871 NC_000003.11:g.10188309T>C True +2246 NC_000003.11:g.10191546T>A False +3012 NC_000003.11:g.10191546T>C False +1807 NC_000003.11:g.10191545A>G True +2329 NC_000003.12:g.10149938delinsAA False +3146 3-10183755-T-G False +1862 NC_000003.11:g.10191482A>G False +2137 3-10191481-GAA-C True +1913 NC_000003.11:g.10191593A>T True +2147 NC_000003.11:g.10191593A>G False +1838 NC_000003.11:g.10183832_10183833delinsGG True +1860 NC_000003.11:g.10183833T>G False +1820 NC_000003.11:g.10188203C>G True +1798 NC_000003.11:g.10188210T>C True +1822 NC_000003.11:g.10188210T>G False +1841 NC_000003.11:g.10188209_10188210insA True +1851 NC_000003.11:g.10188238_10188239delinsTT False +3066 3-10188239-C-T True +2157 NC_000003.11:g.10188240T>C False +1886 NC_000003.11:g.10188240T>G True +3068 NC_000003.11:g.10188238del False +2508 NC_000003.11:g.10188243T>C True +1769 NC_000003.11:g.10188261T>A True +1906 NC_000003.11:g.10188261del True +2559 NC_000003.11:g.10188276delT False +1923 NC_000003.11:g.10188315T>C True +1738 NC_000003.11:g.10191480T>C True +2467 NC_000003.11:g.10191480T>A False +1803 NC_000003.11:g.10191479C>G True +2505 NC_000003.11:g.10191494C>T False +2033 NC_000003.11:g.10191495T>A True +3198 NC_000003.11:g.10191494C>A False +2478 NC_000003.11:g.10191495T>C False +2563 NC_000003.11:g.10191495delT False +3097 NC_000003.11:g.10191512C>T False +1887 NC_000003.11:g.10191513T>C True +2326 NC_000003.12:g.10149828_10149833del False +1748 NC_000003.11:g.10191540T>C True +1997 NC_000003.11:g.10191540T>A True +1888 NC_000003.11:g.10191540T>G True +2070 NC_000003.11:g.10191558T>A False +1776 NC_000003.11:g.10191558T>C True +1808 NC_000003.11:g.10191558T>G True +1852 NC_000003.11:g.10191570T>C True +1861 NC_000003.11:g.10191570T>A True +1924 NC_000003.11:g.10191570T>G True +1836 NC_000003.11:g.10191569C>G True +2139 NC_000003.11:g.10191569del True +1828 NC_000003.11:g.10191570del False +2501 NC_000003.11:g.10191600T>C False +2010 NC_000003.11:g.10191600T>A True +2247 NC_000003.11:g.10191600T>G False +2543 NC_000003.11:g.10191599del False +1944 NC_000003.11:g.10183719T>C False +2020 NC_000003.11:g.10183785T>C True +2308 NC_000003.11:g.10183797T>A False +1793 NC_000003.11:g.10183797T>C True +2549 3-10183797-T-G False +847 NC_000003.11:g.10183531_10183551del True +848 NC_000003.11:g.10183534G>A True +846 NC_000003.11:g.10183532_10183548del True +2868 NC_000003.11:g.10191638A>C False +2177 NC_000003.11:g.10183693G>C False +829 NC_000003.11:g.10183693_10183697del True +1953 NC_000003.11:g.10188250C>A True +2460 NC_000003.11:g.10188250C>G False +2001 NC_000003.11:g.10188249A>G True +2580 NC_000003.11:g.10188249A>C True +1800 NC_000003.11:g.10188247_10188248del True +1868 NC_000003.11:g.10188250_10188251delinsA False +2317 NC_000003.11:g.10188277delC False +2318 NC_000003.12:g.10146595_10146601del False +1917 NC_000003.11:g.10188279_10188297del False +2162 NC_000003.11:g.10188306A>G True +2561 NC_000003.12:g.10146620del True +1770 NC_000003.12:g.10146622del True +2112 NC_000003.11:g.10183763A>G False +1754 NC_000003.11:g.10183763A>C True +2037 NC_000003.11:g.10183764A>T True +1755 NC_000003.11:g.10183764A>G True +1756 NC_000003.11:g.10183764A>C True +2113 NC_000003.11:g.10183763A>T False +849 NC_000003.11:g.10183550A>G True +2878 NC_000003.11:g.10183799A>C False +2149 NC_000003.11:g.10183800A>T False +2058 NC_000003.11:g.10183836del True +1927 NC_000003.11:g.10183838C>G False +1795 NC_000003.11:g.10183840_10183841del True +2118 NC_000003.11:g.10183839C>T False +2866 3-10188271-A-G False +2120 NC_000003.11:g.10188270C>T False +2440 NC_000003.11:g.10188270C>G True +1928 NC_000003.11:g.10188269C>A True +2055 NC_000003.12:g.10146610del True +1962 NC_000003.11:g.10188319A>C True +1782 NC_000003.11:g.10188318C>T True +2427 NC_000003.11:g.10188317C>T False +1771 NC_000003.11:g.10188319del True +2005 NC_000003.11:g.10191523del False +2064 NC_000003.11:g.10191581C>T False +1864 NC_000003.11:g.10191582del False +850 NC_000003.11:g.10183605C>T True +2430 NC_000003.11:g.10183650C>G False +1930 NC_000003.11:g.10183706C>T False +851 NC_000003.11:g.10183704_10183705insC True +1929 NC_000003.11:g.10183707del True +1931 NC_000003.11:g.10183714C>G False +2145 NC_000003.11:g.10183713_10183716del True +2084 NC_000003.11:g.10183773C>T False +1837 NC_000003.11:g.10183772C>T True +1759 NC_000003.11:g.10183787C>G True +2307 NC_000003.11:g.10183788C>A False +1760 NC_000003.11:g.10183788C>T True +1849 NC_000003.11:g.10183788C>G True +1902 NC_000003.11:g.10183787C>T True +1758 NC_000003.11:g.10183785_10183786insC True +2117 NC_000003.11:g.10183815C>G False +2128 NC_000003.11:g.10183822C>G False +2069 NC_000003.11:g.10183821C>T False +1994 NC_000003.11:g.10188251C>T True +1882 3-10188252-A-C False +2125 NC_000003.11:g.10188252A>C True +1883 NC_000003.11:g.10188290C>T True +1781 NC_000003.11:g.10188292_10188293delGC False +1845 NC_000003.11:g.10191497C>T True +1943 3-10191499-G-C False +2880 NC_000003.11:g.10191499G>T False +2079 NC_000003.11:g.10191498A>T True +1856 NC_000003.11:g.10191498A>G True +1810 NC_000003.11:g.10191590C>T True +1752 NC_000003.11:g.10183748C>T True +2041 NC_000003.11:g.10183748del True +1848 NC_000003.11:g.10183817C>T True +1818 NC_000003.11:g.10183818A>C False +3246 NC_000003.12:g.10142135_10142137del True +2007 NC_000003.11:g.10183850C>G True +2044 NC_000003.11:g.10183851G>A True +1840 NC_000003.11:g.10183851G>C True +1796 NC_000003.11:g.10183868C>T True +2143 NC_000003.11:g.10183868delC True +2877 3-10188215-A-T False +1914 NC_000003.11:g.10188215A>G True +2494 3-10188216-G-C False +3244 NC_000003.12:g.10146531_10146532insAC True +1804 NC_000003.11:g.10191488C>T True +2148 NC_000003.11:g.10191488C>A True +1915 NC_000003.11:g.10191488C>G True +1855 NC_000003.11:g.10191489G>C True +1746 NC_000003.11:g.10191489G>A True +1805 NC_000003.11:g.10191506C>G False +1916 NC_000003.11:g.10191507G>T True +2458 NC_000003.11:g.10191507G>C True +1739 NC_000003.11:g.10191507G>A True +1747 NC_000003.11:g.10191506C>T True +1975 3-10191506-CGGAGC-T False +1780 NC_000003.11:g.10191533del True +1827 NC_000003.11:g.10191536A>T True +1907 NC_000003.11:g.10191535del True +631 NC_000003.11:g.10191605C>T True +2302 NC_000003.11:g.10183709_10183710del False +1867 NC_000003.11:g.10183722G>C True +2175 NC_000003.11:g.10183766C>T False +1791 NC_000003.11:g.10183767G>C True +2241 NC_000003.11:g.10183775C>T False +2532 NC_000003.11:g.10183775C>G False +2110 NC_000003.11:g.10183776G>T False +1980 NC_000003.11:g.10183776G>C True +2089 NC_000003.11:g.10183774_10183782del True +1853 NC_000003.11:g.10183861_10183862delinsTT True +2045 NC_000003.11:g.10183862A>T True +1762 NC_000003.12:g.10142178del True +2243 NC_000003.11:g.10183862A>G False +1763 NC_000003.11:g.10183863G>A True +2156 NC_000003.11:g.10183862A>C False +2003 NC_000003.11:g.10183864C>A False +1764 NC_000003.11:g.10183864C>G True +2517 NC_000003.11:g.10183863del False +2541 NC_000003.11:g.10188273C>T False +2004 NC_000003.11:g.10191510delG False +1941 NC_000003.11:g.10191510G>C False +1784 NC_000003.11:g.10191555C>A True +2161 NC_000003.11:g.10191555C>T False +2503 NC_000003.11:g.10191555C>G False +2100 NC_000003.11:g.10191555del False +3135 3-10183643-T-C False +1811 NC_000003.11:g.10183725C>A True +2011 NC_000003.11:g.10183724T>G True +2130 NC_000003.11:g.10183725delC True +1788 NC_000003.11:g.10183725C>T True +1903 NC_000003.11:g.10183724T>C True +3048 NC_000003.11:g.10183724T>A False +1787 NC_000003.11:g.10183725C>G True +2122 NC_000003.11:g.10183734C>A False +1873 NC_000003.11:g.10183733T>C True +2012 NC_000003.11:g.10183734C>G True +1904 NC_000003.11:g.10183745T>C True +1816 NC_000003.12:g.10142061del True +2106 NC_000003.11:g.10183769A>G False +1757 NC_000003.11:g.10183770G>T True +1874 NC_000003.11:g.10183770G>A True +1963 NC_000003.11:g.10183769A>C True +1792 3-10183771-T-G True +2512 NC_000003.11:g.10183770_10183776del False +2511 NC_000003.11:g.10183770del True +2534 NC_000003.11:g.10183874_10183881delinsCG False +2104 NC_000003.11:g.10183876G>C True +2461 NC_000003.11:g.10188323A>C False +2065 NC_000003.12:g.10146639A>G False +2146 NC_000003.11:g.10188323A>T False +2292 NC_000003.11:g.10188328C>T True +1681 NC_000009.11:g.5070054T>G True +4374 NC_000007.14:g.116771990G>T False +4386 NC_000007.14:g.116771989G>A True +2114 NC_000003.11:g.10183872G>A True +2074 NC_000003.11:g.10183872G>T False +2017 NC_000003.12:g.10146513G>A False +2454 NC_000003.12:g.10146513G>T False +2133 NC_000003.11:g.10188196A>C True +2504 NC_000003.11:g.10188196A>G False +1972 NC_000003.11:g.10188321G>A False +1998 NC_000003.11:g.10188321G>C True +2048 NC_000003.11:g.10188321G>T False +2075 NC_000003.11:g.10188322T>C True +1974 NC_000003.11:g.10191470G>A True +2077 NC_000003.11:g.10191470G>C True +1990 NC_000003.11:g.10191470G>T True +2093 NC_000003.11:g.10191469A>C False +2078 NC_000003.11:g.10191469A>G True +1992 NC_000003.11:g.10191469A>T True +2248 NC_000003.11:g.10183829A>G False +1839 NC_000003.11:g.10183844A>C True +2054 NC_000003.11:g.10188228C>T False +1905 NC_000003.11:g.10188226del False +1843 NC_000003.11:g.10188254del True +2085 NC_000003.11:g.10188312C>T False +3130 NC_000003.11:g.10188311A>C False +1745 NC_000003.11:g.10191477C>T True +2323 NC_000003.11:g.10191476delA False +1875 NC_000003.11:g.10188245G>T False +2380 NC_000003.11:g.10188245G>A False +1970 NC_000003.11:g.10188245G>C True +1909 NC_000003.11:g.10191471T>A True +1934 NC_000003.11:g.10191471T>G True +2076 NC_000003.11:g.10188320G>A False +2437 NC_000003.11:g.10191504T>C True +1775 NC_000003.11:g.10191504T>A True +1825 NC_000003.11:g.10191503G>T True +1910 NC_000003.11:g.10191516T>C False +1826 NC_000003.11:g.10191516T>A True +1806 NC_000003.11:g.10191515G>T True +1935 NC_000003.11:g.10191516T>G True +1847 NC_000003.11:g.10191547_10191550del True +2493 NC_000003.11:g.10191588T>G False +1789 NC_000003.11:g.10183727delG False +1936 NC_000003.11:g.10183728T>G False +1999 NC_000003.11:g.10183752T>G True +2270 NG_008212.3:g.5426_5445del False +1937 NC_000003.11:g.10183781G>C False +1815 NC_000003.11:g.10183781G>T True +2101 NC_000003.11:g.10183781G>A True +2068 NC_000003.11:g.10183791T>C False +2513 NC_000003.11:g.10183791T>A False +2432 NC_000003.11:g.10183790_10183791insA True +2249 NC_000003.11:g.10188207G>A False +1821 NC_000003.11:g.10188208G>A False +1767 NC_000003.11:g.10188208G>T True +2521 NC_000003.11:g.10188206T>G False +2522 NC_000003.11:g.10188206T>A False +2523 NC_000003.11:g.10188207G>C False +1294 NC_000003.11:g.10183555G>A True +2151 NC_000003.11:g.10183794G>A True +1908 NC_000003.11:g.10183795G>A True +2124 NC_000003.11:g.10183795G>C False +2039 NC_000003.11:g.10183794_10183796delinsTT True +2242 NC_000003.11:g.10183794G>T False +1761 NC_000003.11:g.10183793T>A True +2056 NC_000003.11:g.10183793T>C True +1966 NC_000003.11:g.10183794G>C True +1766 NC_000003.11:g.10183867C>A True +2818 NC_000003.11:g.10183866A>G False +1865 NC_000003.11:g.10183865T>C True +2006 NC_000003.11:g.10183865T>A False +1968 NC_000003.11:g.10191475T>G True +1946 NC_000003.11:g.10191474A>G True +1967 NC_000003.11:g.10191473T>G True +3182 NC_000003.11:g.10191473T>C False +2013 NC_000003.11:g.10191473T>A True +3193 NC_000003.11:g.10191474A>C False +2453 NC_000003.11:g.10191472_10191477del False +1932 NC_000003.11:g.10191532C>A True +1969 NC_000003.11:g.10191532C>G True +2138 NC_000003.11:g.10191532del True +2067 NC_000003.11:g.10191531A>G True +1846 NC_000003.11:g.10191530T>G True +2066 NC_000003.11:g.10191530T>A True +2115 NC_000003.11:g.10191562C>A False +1809 NC_000003.11:g.10191562C>G True +3125 NC_000003.11:g.10183825C>G False +1933 NC_000003.11:g.10183824A>G True +852 NC_000003.11:g.10183822_10183841del True +2160 NC_000003.11:g.10183822delC True +1741 NC_000003.11:g.10183823T>C True +2484 NC_000003.11:g.10183823T>A False +2480 NC_000003.11:g.10183824A>C False +3022 NC_000003.11:g.10191943G>A False +615 NC_000009.11:g.5070053_5070054insG True +3161 3-10183878-G-A False +877 NC_000020.11:g.58903752C>T True +731 NC_000003.11:g.37056036G>A True diff --git a/analysis/civic/should_be_able_to_normalize_protein_variant_queries.csv b/analysis/civic/should_be_able_to_normalize_protein_variant_queries.csv new file mode 100644 index 0000000..5fc9c29 --- /dev/null +++ b/analysis/civic/should_be_able_to_normalize_protein_variant_queries.csv @@ -0,0 +1,1514 @@ +variant_id gene_name variant_name variant_accepted +748 MLH1 *757L True +467 KDR A1065T True +807 RUNX1 A107P True +3683 JAK1 A1086S False +3030 BCL2 A113G False +3342 KRAS A11_G12insGA True +3544 PTEN A121E False +3528 PTEN A126D False +3565 PTEN A126S False +4131 TP53 A138K False +3416 TP53 A138V False +905 KRAS A146P True +906 KRAS A146T True +322 KRAS A146V True +4134 TP53 A161D False +4116 TP53 A161G False +1114 TP53 A161T True +4136 TP53 A161V False +3976 BRCA1 A1708E False +3994 BRCA1 A1789T False +2929 PRPS1 A190T True +2928 PRPS1 A190V False +610 MTOR A2034V True +3147 NTRK2 A203T False +1169 ATM A2062V True +1522 CDKN2A A20P False +258 MTHFR A222V True +1171 ATM A2274T False +1217 ERBB3 A232V False +3708 AR A234T False +1050 TP53 A276V True +996 EGFR A289V True +4402 CDH1 A298T False +4126 TP53 A347G False +4023 FGFR3 A391E True +752 MLH1 A424T True +1588 SMO A459V False +4248 PTPN11 A461T False +1558 KIT A502_Y503insAY True +2826 BRAF A598V True +1646 POLE4 A59E False +760 MLH1 A681V True +4415 EZH2 A682G True +4414 EZH2 A692V True +2255 EGFR A702S False +1198 BRAF A728V True +3718 AR A748V False +2332 EGFR A750T False +1515 EGFR A763_Y764insFQEA True +3725 AR A765T False +2658 ERBB2 A775_G776insYVMA False +3591 RIT1 A77P False +3592 RIT1 A77S False +990 KIT A829P True +4127 TP53 A83E False +1474 EGFR A859T False +1187 EGFR A864T True +3751 ARHGAP35 A865_L870delinsV False +4129 TP53 A86E False +4128 TP53 A86T False +2939 PRPS1 A87T True +153 FOXP1 AMPLIFICATION True +154 REL AMPLIFICATION True +204 NCOA3 AMPLIFICATION True +224 TTF1 AMPLIFICATION True +2655 MYB AMPLIFICATION True +842 BRAF APC False +2758 BRCA1 ATM False +18 CCND1 Amplification True +180 AURKA Amplification True +187 CCNE1 Amplification True +190 EGFR Amplification True +212 PIK3CA Amplification True +219 TERT Amplification True +251 BIRC7 Amplification True +267 FGFR1 Amplification True +270 MET Amplification True +298 MYCN Amplification True +306 ERBB2 Amplification True +321 MAPK1 Amplification True +330 NOTCH1 Amplification True +358 RSF1 Amplification True +371 TOP1 Amplification True +379 TYMS Amplification True +407 ABCC3 Amplification True +409 ASNS Amplification True +553 CDK4 Amplification True +573 RICTOR Amplification True +586 KIT Amplification True +591 RAF1 Amplification True +592 KRAS Amplification True +629 FGFR2 Amplification True +630 FGF3 Amplification True +635 AKT2 Amplification True +716 PDGFRA Amplification True +1261 MDM2 Amplification False +1268 MDM4 Amplification False +1269 BRAF Amplification True +1276 SMO Amplification False +1280 NTRK1 Amplification True +1281 NTRK3 Amplification True +1684 PSMD4 Amplification False +1685 CDK6 Amplification False +2205 FLT4 Amplification False +2240 TLK2 Amplification True +2397 CRKL Amplification False +2550 NRAS Amplification False +2564 MYC Amplification False +2598 IRS2 Amplification False +2619 FLT3 Amplification False +2637 KDR Amplification False +2746 CCND2 Amplification False +2747 CCND3 Amplification False +2844 MITF Amplification False +2906 FGFR3 Amplification False +2907 FGFR4 Amplification False +3687 KMT2A Amplification False +4301 ALK Amplification True +4423 TBXT Amplification False +4331 ALK C1156Y True +627 MAP2K1 C121S True +4113 TP53 C124R True +3547 PTEN C124S False +2840 MAP2K2 C125S False +198 FOXL2 C134W True +2719 TP53 C135F False +924 TP53 C135W True +1111 TP53 C135Y False +3382 PTEN C136R True +1094 TP53 C141W False +2713 MTOR C1483F False +3413 MTOR C1483R False +543 MTOR C1483Y True +3389 TP53 C176F False +4118 TP53 C176S False +1116 TP53 C176Y False +248 TERT C228T True +3393 TP53 C238F False +2648 TP53 C238Y True +1062 TP53 C242F False +1063 TP53 C242S False +1064 TP53 C242Y True +1172 ATM C2488Y True +4004 TERT C250T False +4124 TP53 C275F False +917 TP53 C275Y False +4145 TP53 C277Y False +1647 POLD1 C284Y True +3357 FGFR2 C342R False +3358 FGFR2 C342Y False +931 PIK3CA C420R True +1586 SMO C469Y False +1639 ABL1 C475V True +4017 BTK C481R False +168 BTK C481S True +4016 BTK C481Y False +3605 EZH2 C576W False +3337 PIK3CA C604R False +1260 RET C609Y True +1700 RET C634R False +112 RET C634W True +2936 PRPS1 C77S True +3003 EGFR C797G False +415 EGFR C797S True +1574 EGFR C797Y True +1264 KIT C809G True +3756 BAP1 C91S False +2789 PIK3CA C971R False +1660 MET D1010H False +1651 MET D1010N False +1649 MET D1010Y False +3062 BCL2 D103E False +3061 BCL2 D103V False +3058 BCL2 D103Y False +3380 CDKN2A D108H False +3288 CDKN2A D108N False +2791 CDKN2A D108Y False +4015 PLCG2 D1140E False +649 MET D1228N True +798 MET D1228V True +2935 PRPS1 D139G True +3349 SPOP D140G False +3553 PTEN D162G False +135 NOTCH1 D1642H True +1168 ATM D1682H True +2196 DICER1 D1709E True +2195 DICER1 D1709G True +2051 DICER1 D1709N True +3802 TSC2 D1734E False +3980 BRCA1 D1739G False +3981 BRCA1 D1739V False +2197 DICER1 D1810H False +2199 DICER1 D1810N False +2198 DICER1 D1810Y False +2920 PRPS1 D183E True +2933 PRPS1 D183H False +1160 ATM D1930V True +634 STK11 D194E True +806 RUNX1 D198Y True +1641 ROS1 D2033N False +3706 AR D221H False +3401 TP53 D259V True +3610 BRCA2 D2611G False +3625 BRCA2 D2723A False +3631 BRCA2 D2723G False +3639 BRCA2 D2723H False +1044 TP53 D281E True +1045 TP53 D281G False +3792 TP53 D281N True +4146 TP53 D281Y False +3495 ERBB3 D297Y False +650 CASP8 D302H True +3611 BRCA2 D3073G False +661 BRCA2 D3095E True +4222 AKT1 D323G False +3256 CTNNB1 D32Y False +1653 PIK3CA D350G True +3338 PIK3CA D350N False +2852 SMAD4 D351H False +2995 TP53BP1 D353E False +1606 ABL1 D363Y False +240 NT5C2 D407A True +855 KIT D419del False +2468 PRKCB D427N True +1560 SMO D473G False +299 SMO D473H True +1561 SMO D473Y False +3959 SMAD4 D493H False +3713 AR D528G False +2858 SMAD4 D537Y False +47 ESR1 D538G True +1399 PIK3CA D549N False +1547 KIT D579_H580insIDPTQLPYD False +977 KIT D579del True +4341 FLT3 D593del False +579 BRAF D594A True +2799 BRAF D594E False +611 BRAF D594G True +2832 BRAF D594H False +2833 NECTIN4 D594H False +2398 BRAF D594K True +1107 BRAF D594N False +580 BRAF D594V True +3698 FGFR3 D617G False +2573 PTPN11 D61Y False +468 KDR D717V True +1013 EGFR D761N False +712 EGFR D761Y True +35 ERBB2 D769H True +36 ERBB2 D769Y True +1512 EGFR D770_N771insG True +1514 EGFR D770_N771insGL True +1566 EGFR D770_N771insGT True +1569 EGFR D770_N771insNPG True +1445 EGFR D770_N771insSVD True +2214 EGFR D770delinsGY True +1559 KIT D816E True +4419 KIT D816F False +1402 KIT D816G False +983 KIT D816H True +65 KIT D816V True +984 KIT D816Y False +1265 KIT D820A True +2736 KIT D820E False +1266 KIT D820G True +986 KIT D820Y True +1397 FLT3 D835E False +4340 FLT3 D835G False +612 FLT3 D835H True +3075 FLT3 D835I True +4339 FLT3 D835N False +1302 FLT3 D835V True +3011 FLT3 D835Y True +3167 FLT3 D839A False +3160 FLT3 D839G False +3169 FLT3 D839H False +3168 FLT3 D839N False +98 PDGFRA D842I True +99 PDGFRA D842V True +100 PDGFRA D842Y True +102 PDGFRA D842_I843delinsVM True +1518 PDGFRA D842_M844del False +3374 CDKN2A D84G False +3334 CDKN2A D84H False +3285 CDKN2A D84N False +3375 CDKN2A D84V False +3333 CDKN2A D84Y False +2574 SETBP1 D868N False +3538 PTEN D92A False +3539 PTEN D92E False +3540 PTEN D92G False +3541 PTEN D92H False +3542 PTEN D92V False +3293 PIK3CA D939G False +2414 MAP2K1 E102_I103delEI False +3290 PIK3CB E1051K False +3464 EGFR E114K False +566 MAP2K7 E116K True +4329 ALK E1210K False +2050 DICER1 E1705K True +544 MTOR E1799K True +4 AKT1 E17K True +1227 AKT3 E17K True +3585 TP53 E180K False +2200 DICER1 E1813G False +2201 DICER1 E1813K False +2052 DICER1 E1813Q True +3707 AR E198G False +572 MTOR E2014K True +1626 MAP2K1 E203K False +1162 ATM E2187* True +3780 TP53 E224K True +4427 MTOR E2419K True +3 ABL1 E255K True +1601 ABL1 E258D False +3772 TP53 E258K True +1552 MAPK1 E278E False +1603 ABL1 E281K False +1043 TP53 E285K False +3462 TP53 E285V False +915 TP53 E286K True +3621 BRCA2 E3002K False +3496 ERBB4 E317K False +320 MAPK1 E322K True +2853 SMAD4 E330A False +3521 SMAD4 E330K False +1648 POLD1 E374K True +1674 ESR1 E380Q False +691 ERRFI1 E384* True +3336 PIK3CA E39K False +4306 KLF5 E419K True +4307 KLF5 E419Q True +1619 ABL1 E450A False +1496 ABL1 E450G False +1617 ABL1 E450K False +1620 ABL1 E453V False +1621 ABL1 E459G False +3692 FGFR3 E466K False +3343 SPOP E47K False +3682 JAK1 E483D False +773 MSH2 E483G True +3345 SPOP E50K False +2282 DROSHA E518K False +103 PIK3CA E542K True +933 PIK3CA E542Q False +882 PIK3CA E545A False +934 PIK3CA E545D False +883 PIK3CA E545G True +104 PIK3CA E545K True +881 PIK3CA E545Q True +884 PIK3CA E545V False +2709 PIK3CA E545X False +955 KIT E554D False +3449 BRAF E585K False +1631 FLT3 E588_Y589INSKYFYVDFRE False +4106 TP53 E68G True +4420 HBB E6V False +1412 EGFR E709K False +1413 EGFR E709Q False +1572 EGFR E734Q True +724 EGFR E746G True +1431 EGFR E746K False +1005 EGFR E746V False +1002 EGFR E746_A750del True +1009 EGFR E746_S752delinsD False +4280 EGFR E746_S752insV False +1004 EGFR E746_T751delinsA False +1214 EGFR E746_T751delinsVA False +3754 BACH2 E788K False +4476 TET2 E796K False +3504 ERCC2 E79D False +4320 NFE2L2 E79K False +3960 NFE2L2 E79Q False +1500 PIK3CA E81K True +3430 NFE2L2 E82D False +4107 SOS1 E846K False +1482 EGFR E868G True +3505 ERCC2 E86Q False +1390 EGFR E884K False +3332 CDKN2A E88K False +3537 PTEN E91A False +3484 FN1 EDB False +4005 EWSR1 EWSR1-ERG False +1158 ATM F1025L True +3082 BCL2 F104I True +3028 BCL2 F104L False +3027 BCL2 F104S False +1492 ALK F1174C False +8 ALK F1174L True +1505 ALK F1174V False +549 ALK F1245C True +1295 ALK F1245V True +1174 NOTCH1 F1592C False +1127 NOTCH1 F1592S False +2714 MTOR F1888L False +470 MTOR F2108L True +457 FCGR3A F212V True +2285 CRLF2 F232C False +2802 BRAF F247L False +1053 TP53 F270S True +1164 ATM F2732V True +1507 ABL1 F311I True +1028 ABL1 F317L True +1525 ABL1 F317V True +2063 STK11 F354L False +3516 FGFR3 F384L False +2616 EGFR F404I False +2617 EGFR F404V False +1538 ABL1 F486Y False +3240 KIT F504A False +1270 MAP2K1 F53L False +2839 MAP2K1 F53Y False +4223 AKT1 F55Y False +1398 MAP2K2 F57C False +3450 BRAF F594L False +1121 BRAF F595L False +3468 NTRK3 F617L True +3071 FLT3 F691L True +2587 JAK2 F694L True +3593 RIT1 F82L False +1881 ATM F858L False +175 AR F877L True +3536 PTEN F90L False +3667 PIK3CA F930S True +3437 PIK3CA G1007R False +3026 BCL2 G101A False +2960 BCL2 G101V True +1501 PIK3CA G1049A False +940 PIK3CA G1049R True +939 PIK3CA G1049S False +3341 KRAS G10_A11insG True +1673 ERBB4 G1109C False +2798 ALK G1128A False +171 ALK G1202R True +2813 ALK G1202del False +308 ALK G1269A True +4334 ALK G1269S False +3549 PTEN G127E False +2835 MAP2K1 G128V False +3563 PTEN G129E False +3562 PTEN G129R False +3561 PTEN G129V False +148 KRAS G12A True +78 KRAS G12C True +897 NRAS G12C True +79 KRAS G12D True +878 NRAS G12D True +1387 HRAS G12D False +530 KRAS G12R True +898 NRAS G12S False +913 KRAS G12S True +425 KRAS G12V True +1175 NRAS G12V False +1394 HRAS G12V False +2873 MAP2K2 G132D False +2874 MAP2K2 G132S False +895 NRAS G13C False +911 KRAS G13C False +81 KRAS G13D True +93 NRAS G13D True +274 HRAS G13D True +896 NRAS G13R True +1393 HRAS G13R False +1395 KRAS G13R False +1396 KRAS G13S False +1317 NRAS G13V False +1489 HRAS G13V False +1517 KRAS G13V True +2676 EP300 G1506V False +3419 TP53 G154S False +3559 PTEN G165E False +3560 PTEN G165V False +3973 BRCA1 G1706A False +3972 BRCA1 G1706E False +2922 PRPS1 G174E False +3993 BRCA1 G1770V False +3793 TP53 G177E False +1271 ROS1 G2032R True +3152 GNA11 G209P False +3153 GNAQ G209P False +1060 TP53 G244S True +3397 TP53 G244V False +1036 TP53 G245D True +879 TP53 G245S True +3331 LZTR1 G248R False +2279 CRLF2 G24R False +1599 ABL1 G250V False +3523 SMAD4 G252* False +141 DDR2 G253C True +3615 BRCA2 G2585R False +3628 BRCA2 G2609D False +4144 TP53 G262C False +3773 TP53 G262D True +3774 TP53 G266E True +1055 TP53 G266R True +4122 TP53 G266V True +2838 MAP2K1 G276W False +3613 BRCA2 G2793E False +3616 BRCA2 G2793R False +3791 TP53 G279E True +703 ERBB3 G284R True +3623 BRCA2 G3076E False +3620 BRCA2 G3076V False +38 ERBB2 G309A True +3457 NFE2L2 G31A True +2283 ACVR1 G328E True +1686 ACVR1 G328V True +2280 ACVR1 G328W True +1657 ABL1 G340L True +3492 CTNNB1 G34E False +3253 CTNNB1 G34R False +3379 H3-3A G34R True +2576 CTNNB1 G34V False +3378 H3-3A G34V False +2421 H3-3A G34W True +3662 ACVR1 G356D True +2788 PIK3CA G363A False +3286 PTEN G36R False +2406 FGFR3 G370C True +3381 PIK3R2 G373R True +2405 FGFR3 G380R True +3522 SMAD4 G386D False +3520 SMAD4 G419V False +3432 BRAF G463E True +3442 BRAF G463V False +1106 BRAF G464V True +3443 BRAF G465A False +2603 EGFR G465E False +443 EGFR G465R True +2604 EGFR G465V False +1196 BRAF G466A False +2792 BRAF G466E False +2222 BRAF G466V True +3441 BRAF G468A False +992 BRAF G469A True +993 BRAF G469E True +840 BRAF G469R False +3425 BRAF G469S False +841 BRAF G469V False +2221 BRAF G496A True +1584 SMO G497W False +142 DDR2 G505S True +1624 ABL1 G514S False +4007 DDX41 G530D False +1678 FBXW7 G579W False +2823 BRAF G593D False +2690 NTRK1 G595R False +694 BRAF G596C True +1627 BRAF G596R True +1650 BRAF G596V False +997 EGFR G598V True +2223 BRAF G606E True +2855 NTRK3 G623E False +2691 NTRK3 G623R False +3215 FGFR4 G636C False +3699 FGFR3 G637W False +3488 EGFR G63R False +759 MLH1 G65D True +757 MLH1 G67R True +1692 FGFR3 G691R False +4030 FGFR3 G697C False +2817 FLT3 G697R False +3212 FLT3 G697S False +999 EGFR G719A True +1420 EGFR G719D True +134 EGFR G719S True +317 EGFR G724S True +3346 SPOP G75R False +144 DDR2 G774V True +816 ERBB2 G776L True +4470 ERBB2 G776V False +3649 KDR G800D False +3650 KDR G800R False +4298 FGFR3 G802_X807del False +3226 RET G810C False +1016 EGFR G810S False +3227 RET G810S False +3651 KDR G843D False +772 HOXB13 G84E True +865 PDGFRA G853D True +351 SETBP1 G870S True +1151 PIK3CA H1047L True +107 PIK3CA H1047R True +2710 PIK3CA H1047X True +938 PIK3CA H1047Y False +2957 MET H1094L False +4112 TP53 H115Y True +3546 PTEN H123D False +2872 MAP2K2 H123Q False +3803 SMAD4 H132Y False +456 FCGR2A H167R True +3963 BRCA1 H1686Q False +3962 BRCA1 H1686R False +4138 TP53 H168Q False +4137 TP53 H168R False +3783 TP53 H168Y True +4103 TP53 H178P True +1082 TP53 H179R True +1083 TP53 H179Y True +3996 BRCA1 H1862L False +4119 TP53 H193L False +283 MTOR H1968Y True +1595 ABL1 H201L False +4335 TP53 H214R False +1446 EGFR H773_V774insH True +1513 EGFR H773_V774insNPH True +864 PDGFRA H845Y True +874 ERBB2 H878Y True +3529 PTEN H93D False +3530 PTEN H93Q False +3340 PTEN H93R False +3531 PTEN H93Y False +4323 CBL H94Y False +259 GSTP1 I105V True +263 ABCB1 I1145I True +588 ALK I1171N True +589 ALK I1171S True +3371 ALK I1171T True +3545 PTEN I122S False +787 CHEK2 I157T True +3768 TP53 I162F True +3555 PTEN I168F False +458 FCGR2B I232T True +1598 ABL1 I242T False +3758 U2AF1 I24T False +3630 BRCA2 I2627F False +3255 CTNNB1 I35K False +1235 PIK3CA I391M True +1585 SMO I408V False +1615 ABL1 I418S False +1614 ABL1 I418V False +2599 EGFR I462K False +2600 EGFR I462R False +3448 BRAF I462S False +2608 EGFR I491K False +2609 EGFR I491R False +4022 FGFR3 I538F False +143 DDR2 I638F True +2677 ERBB2 I654V False +758 MLH1 I68S True +2937 PRPS1 I72V True +2259 EGFR I744_K745insKIPVAI False +3664 ERBB2 I767M False +3572 FLT3 I836S False +3573 FLT3 I836T False +101 PDGFRA I843DEL True +755 MSH6 I972F False +1234 PIK3CA K111N True +1120 KRAS K117N False +3584 TP53 K120E False +3596 TP53 K120R False +3548 PTEN K125E False +3564 PTEN K128N False +3764 TP53 K139E True +770 MSH2 K172* True +2921 PRPS1 K176N True +3023 PML K227_T233del False +2815 H3C2 K27M True +3939 H3-3A K27M False +3944 H3C14 K27M False +3594 H3-3A K27R False +2416 H3-3A K28M True +1155 ATM K293* True +3402 TP53 K305M False +4147 TP53 K305N False +2871 BRCA2 K3326* True +239 NT5C2 K359Q True +3745 CTCF K365T True +2420 H3-3B K36M True +3440 KLF4 K409Q False +2775 BRAF K439Q False +2776 BRAF K439T False +2605 EGFR K467N False +455 EGFR K467T True +581 BRAF K483M True +2622 KIT K484_G487DEL True +2607 EGFR K489E False +2606 EGFR K489Q False +949 KIT K550_K558del True +2696 KIT K550_K559DEL True +948 KIT K550_W557del True +963 KIT K558Q False +965 KIT K558R False +964 KIT K558_V559del True +1549 KIT K558delinsNP True +1272 MAP2K1 K57N True +824 MAP2K1 K57T False +3455 BRAF K600E False +584 BRAF K601E True +733 MLH1 K618DEL True +978 KIT K642E True +2592 KIT K642R False +4024 FGFR3 K650D True +1400 FGFR3 K650E True +4025 FGFR3 K650L True +4013 FGFR3 K650M True +3695 FGFR3 K650N True +4019 FGFR3 K650Q True +4021 FGFR3 K650T False +2947 FGFR2 K660E False +3166 FLT3 K663Q False +114 SF3B1 K666N True +565 SF3B1 K700E True +3490 EGFR K708R False +3714 AR K720E False +1638 EGFR K745_E749delKELRE False +264 ERCC2 K751Q True +1312 ERBB2 K753E False +4409 EGFR K754E True +4319 SMARCA2 K755R True +1314 ERBB2 K755S False +723 EGFR K757R True +1895 EGFR K806E True +802 RUNX1 K83E True +3666 PIK3CA K944N True +3669 PIK3CA K966E True +4111 TP53 L111R True +1554 ALK L1152P False +307 ALK L1152R True +4332 ALK L1152V False +4324 ALK L1196M True +1553 ALK L1196Q False +1275 ALK L1198F True +1556 ALK L1198P False +3031 BCL2 L119V False +3032 MYOD1 L122R True +2168 RAD50 L1237F True +3660 CYSLTR2 L129Q False +1099 TP53 L130V False +3078 VHL L135* False +4114 TP53 L139N True +4273 BRCA1 L1407P False +1032 NOTCH1 L1574P False +1145 NOTCH1 L1574Q False +1142 NOTCH1 L1585R False +4449 ERBB2 L15F False +1031 NOTCH1 L1600P False +1140 NOTCH1 L1600Q False +1034 NOTCH1 L1678P False +3335 CDKN2A L16P False +2675 MSH2 L173P False +3982 BRCA1 L1764P False +2919 PRPS1 L191F True +1078 TP53 L194P False +3392 TP53 L194R False +2716 MTOR L2230V False +140 DDR2 L239R True +1163 ATM L2427P True +3414 MTOR L2427Q False +3755 BACH2 L24P False +3624 BRCA2 L2510P False +3771 TP53 L252F True +3801 TP53 L257P True +3640 BRCA2 L2647P False +3642 BRCA2 L2653P False +3612 BRCA2 L2654P False +424 MYD88 L265P True +3638 BRCA2 L2688P False +1602 ABL1 L273M False +3617 BRCA2 L2792P False +1506 ABL1 L298V True +3643 PIM1 L2V True +4125 TP53 L305M False +3775 TP53 L308M True +4322 NFE2L2 L30F False +3776 TP53 L323P True +3580 TP53 L330P True +3581 TP53 L330R True +3583 TP53 L344P True +1570 SMO L412F True +4313 POLE L424I False +4158 POLE L424V False +2842 MAP2K2 L46F False +2804 BRAF L485F False +658 BRAF L505H True +2793 BRAF L525R False +1191 AKT1 L52R False +46 ESR1 L536Q True +1675 ESR1 L536R False +72 KIT L576P True +1540 PDGFRA L579M False +3705 AR L57Q False +3451 BRAF L596V False +583 BRAF L597Q True +288 BRAF L597R True +582 BRAF L597S True +585 BRAF L597V True +2401 FGFR3 L608V False +1309 ERBB2 L638S False +139 DDR2 L63V True +2999 EGFR L718Q False +3000 EGFR L718V False +3717 AR L744F False +1891 EGFR L747P True +1006 EGFR L747_A750delinsP False +1012 EGFR L747_P753delinsS True +890 EGFR L747_S752del False +1580 EGFR L747_S752delinsQ True +1007 EGFR L747_T751delLREAT False +1010 EGFR L747_T751delinsP False +1008 EGFR L747_T751delinsQ False +1313 ERBB2 L753E False +1304 ERBB2 L755P False +39 ERBB2 L755S True +40 ERBB2 L755W True +37 ERBB2 L755_T759del True +1308 ERBB2 L768S False +4477 BAX L76R False +3004 EGFR L792H False +1457 EGFR L838P True +1018 EGFR L838V True +3648 KDR L840F False +1473 EGFR L858Q False +33 EGFR L858R True +1020 EGFR L861Q True +1477 EGFR L861R True +496 ERBB2 L866M True +2330 ERBB2 L869R False +3670 PIK3CA L938* True +937 PIK3CA M1043I False +2940 PRPS1 M115T True +3301 SPOP M117I False +3280 SPOP M117V False +3372 MET M1250T False +3966 BRCA1 M1628T False +3965 BRCA1 M1652I False +4401 BRCA1 M1775K False +4400 BRCA1 M1775R False +1248 BRCA2 M1I True +747 MLH1 M1L True +1247 BRCA2 M1R True +609 MTOR M2327I True +1066 TP53 M237I True +1597 ABL1 M237V False +3396 TP53 M243T False +3398 TP53 M246A False +3789 TP53 M246L True +4105 TP53 M246R False +3399 TP53 M246T False +1610 ABL1 M388L False +1622 ABL1 M472I False +769 MLH1 M490T True +1288 JAK3 M511I False +3515 FGFR3 M528I False +201 KIT M541L True +951 KIT M552_W557DEL False +3165 FLT3 M664I False +2745 EGFR M766Q False +1664 EGFR M766_A767insAI True +2213 EGFR M766_A767insASV True +818 ERBB2 M774DELINSWLV True +3588 RIT1 M90I False +113 RET M918T True +3435 MYOD1 MYOD1 L122R False +3438 PIK3CA N1044K False +2924 PRPS1 N114D False +2843 MAP2K2 N126D False +778 SLCO1B1 N130D True +2923 PRPS1 N144S True +3281 ERCC2 N238S False +3394 TP53 N239D False +3787 TP53 N239S True +3395 TP53 N239T False +244 ATM N2875H True +3641 BRCA2 N3124I False +930 PIK3CA N345K True +3679 ETV6 N385_R418del False +3681 JAK1 N451S False +2794 BRAF N486_P490del True +3237 KIT N505I False +3238 KIT N505R False +3216 FGFR4 N535K False +4028 FGFR3 N540D False +3693 FGFR3 N540K False +3694 FGFR3 N540S False +515 FGFR1 N546K True +2780 FGFR2 N549H False +545 FGFR2 N550K True +751 MLH1 N551T True +1652 PIK3R2 N561D True +4014 PLCG2 N571S False +3444 BRAF N580S False +1186 BRAF N581S True +3053 FLT3 N676K False +3719 AR N756D False +3304 EGFR N771_P772insL True +1662 EGFR N771delinsVH False +987 KIT N822H True +1263 KIT N822K True +1188 EGFR N826S True +1896 EGFR N826Y True +3201 FLT3 N841I False +3213 FLT3 N841K False +3308 FLT3 N841T False +1899 EGFR N842S True +873 ERBB2 N857S True +3532 PTEN N94I False +2837 MAP2K1 P124L False +82 MAP2K1 P124S True +734 MLH1 P138T True +761 MSH6 P138T True +1644 PXDNL P1460T False +3418 TP53 P151A False +1093 TP53 P151H True +3765 TP53 P151S True +3767 TP53 P152L True +3794 TP53 P152T True +3556 PTEN P169H False +3785 TP53 P177F True +3786 TP53 P177H True +3784 TP53 P177S True +3299 PPP2R1A P179R True +3997 BRCA1 P1812R False +402 NQO1 P187S True +4141 TP53 P190H False +1080 TP53 P190L False +813 ETV6 P214L False +4473 ARAF P216A False +3778 TP53 P219H True +284 MTOR P2213S True +3318 TP53 P250L True +2905 FGFR2 P253R True +1218 ERBB3 P262H False +3005 TP53 P278A False +1049 TP53 P278S True +4315 POLE P286H False +1830 POLE P286R True +3570 CCND1 P287S False +3571 CCND1 P287T False +367 RAC1 P29S True +3711 AR P340L False +3266 KRAS P34R False +3289 CTCF P378L False +3602 ATXN7 P40Q False +1291 JAK1 P429S False +3603 ATXN7 P42_P43insP False +1616 ABL1 P441L False +3458 PIK3CA P447_L455del False +4478 AXIN2 P455K False +294 PIK3CA P471L True +504 TP53 P47S True +1623 ABL1 P480L False +3377 CDKN2A P48L False +2796 BRAF P490_Q494del False +3712 AR P504L False +1582 EGFR P546S False +950 KIT P551L False +1497 KIT P551_E554delPMYE True +976 KIT P577L False +862 PDGFRA P577S True +2738 KIT P577_D579DEL False +3489 EGFR P596L False +2180 TSPYL1 P62S False +2990 BRCA2 P655R False +531 TP53 P72R True +2224 BRAF P731T True +460 EGFR P753S True +2217 EGFR P772_H773insH False +1667 EGFR P772_H773insYNP True +1668 EGFR P772_V774insPHV True +2697 PAX5 P80R False +3644 PIM1 P81S True +3384 CDKN2A P81T False +1465 EGFR P848L False +480 DNMT3A P904L False +3348 SPOP P94A False +4304 SRSF2 P95H True +3533 PTEN P95L False +4303 SRSF2 P95L True +3534 PTEN P96Q False +3761 TP53 P98L True +3760 TP53 P98S True +3302 TYK2 Pro1104Ala False +1159 ATM Q1084* False +469 TSC2 Q1178* True +260 ABCG2 Q141K True +3777 TP53 Q144P True +4132 TP53 Q144Q False +1246 BRCA1 Q1467* True +753 MLH1 Q149* True +4135 TP53 Q167R False +1654 NRAS Q179X True +1593 PTCH1 Q17X False +4413 GNA11 Q209L True +604 GNAQ Q209P True +479 KRAS Q22* True +1520 MTOR Q2223K False +1643 SCN8A Q225X False +2700 CBL Q294E False +3601 ATXN7 Q30R False +261 XRCC1 Q399R True +3600 ATXN7 Q39P False +3590 RIT1 Q40L False +1510 ARID1A Q456* True +1564 SMO Q477E False +614 JAK1 Q503* True +3663 BRAF Q524L False +886 PIK3CA Q546E False +885 PIK3CA Q546K True +887 PIK3CA Q546P False +888 PIK3CA Q546R False +1541 KIT Q556_I571DEL False +83 MAP2K1 Q56P True +655 MAP2K1 Q56_V60del True +975 KIT Q575L False +1104 KRAS Q61E False +893 NRAS Q61H True +907 KRAS Q61H True +427 NRAS Q61K True +910 KRAS Q61K True +1392 HRAS Q61K False +95 NRAS Q61L True +854 HRAS Q61L False +908 KRAS Q61L True +1103 KRAS Q61P False +96 NRAS Q61R True +909 KRAS Q61R True +1391 HRAS Q61R False +981 KIT Q694K False +3576 ERBB2 Q709L False +3433 RRAS2 Q72L False +1592 PTCH1 Q787X False +3726 AR Q798E False +169 AKT1 Q79K True +3589 RIT1 Q79L False +1157 ATM Q984E False +4000 RAF1 QKI-RAF1 True +741 MLH1 R100* True +2774 MET R1004G True +3653 KDR R1022Q False +1594 PIK3CA R1023Q False +3350 KDR R1032Q True +702 ERBB3 R103G True +714 TSC1 R1062W True +994 EGFR R108K True +3282 TP53 R110L False +4318 SMARCA2 R1159Q True +1661 ALK R1192P False +3498 ERBB3 R1202W False +2645 KDM6A R1213* False +3300 SPOP R121Q False +776 MSH6 R1242C True +767 MSH6 R1242H True +9 ALK R1275Q True +3292 NF1 R1276Q False +3060 BCL2 R129L False +636 PTEN R130* True +1037 PTEN R130G False +899 PTEN R130Q False +59 IDH1 R132C True +927 IDH1 R132G False +420 IDH1 R132H True +880 IDH1 R132L False +4433 IDH1 R132Q False +928 IDH1 R132S False +4102 TP53 R156H True +3795 TP53 R156P True +1170 ATM R1575H False +3967 BRCA1 R1589P False +4133 TP53 R158C False +4115 TP53 R158G True +1695 TP53 R158H True +1699 TP53 R158L True +3543 PTEN R15K False +1628 NF1 R163X False +1207 KRAS R164Q True +814 DDX41 R164W True +3470 EGFR R165Q False +4397 BRCA1 R1699Q False +3971 BRCA1 R1699W False +2364 PREX2 R172I True +63 IDH2 R172K True +838 PTEN R173C True +3420 TP53 R174K False +1085 TP53 R174W False +116 TP53 R175H True +3796 TP53 R181C True +3797 TP53 R181G True +3798 TP53 R181H True +4140 TP53 R181L False +3390 TP53 R181P True +4412 GNA11 R183C True +471 RAD51D R186* True +249 XRCC1 R194W True +4142 TP53 R196Q False +826 GNAS R201C True +1319 GNAS R201H True +4305 CIC R201W False +2857 ROS1 R2033N False +1161 ATM R2034P False +3661 ACVR1 R206H True +3575 PMS2 R20Q False +2711 TP53 R213* False +1109 TP53 R213P True +4121 TP53 R213Q False +1683 ALK R214H False +3439 MTOR R2152C False +3431 CIC R215W False +3344 EGFR R222C True +754 MLH1 R226* True +136 NOTCH1 R2327W True +110 PTEN R233* True +1252 BRCA2 R2336P True +2896 NT5C2 R238W True +1156 ATM R2459C False +2403 FGFR3 R248C True +3069 NTRK3 R248C False +920 TP53 R248L False +117 TP53 R248Q True +118 TP53 R248W True +3400 TP53 R249G False +1696 TP53 R249S True +556 CDK4 R24C True +3961 EGFR R252C False +2275 ACVR1 R258G False +3618 BRCA2 R2659G False +749 MLH1 R265G True +3421 TP53 R267Q False +121 TP53 R273C True +122 TP53 R273H True +918 TP53 R273L True +2753 PRKN R275W False +3619 BRCA2 R2784Q False +3626 BRCA2 R2784W False +1697 TP53 R280K True +1698 TP53 R280T True +1108 TP53 R282L True +916 TP53 R282W True +3799 TP53 R283H True +3422 TP53 R283P False +3608 BRCA2 R2842C False +903 ATM R3008C True +4148 TP53 R306E False +768 PMS2 R315* True +3423 TP53 R337C False +3424 TP53 R337H False +1112 TP53 R337L False +3582 TP53 R337P True +4149 TP53 R337S False +3579 TP53 R342P True +1656 ABL1 R351W True +2276 AMER1 R358X False +2851 SMAD4 R361C True +238 NT5C2 R367Q True +812 ETV6 R369Q False +3757 SMAD3 R373H False +3339 CTCF R377H False +727 MSH2 R383* True +1680 RAF1 R391W True +811 ETV6 R399C False +3463 PALB2 R414X False +3678 ETV6 R418G False +454 EGFR R451C True +3144 NTRK2 R458G False +3447 BRAF R461I False +3671 FBXW7 R465C False +2647 FBXW7 R465H False +3672 FBXW7 R479Q False +3519 SMAD4 R496H False +1503 FBXW7 R505C False +1504 FBXW7 R505H False +3673 FBXW7 R505L False +2803 BRAF R558Q False +1679 FBXW7 R658Q False +3696 FGFR3 R669G False +3697 FGFR3 R669Q False +42 ERBB2 R678Q True +2829 JAK2 R683G False +3604 EZH2 R690C False +2333 EGFR R705K True +3716 AR R726L False +4404 CDH1 R732Q False +3485 DNMT3A R736H False +1181 EGFR R776C True +1017 EGFR R831H True +2741 EGFR R832L False +863 PDGFRA R841K True +2782 TEK R849W False +3376 CDKN2A R87P False +1125 DNMT3A R882H False +1124 DNMT3A R882P False +929 PIK3CA R88Q True +43 ERBB2 R896C True +3434 PIK3CA R93Q False +1178 PIK3CA R93W True +502 KDR R961W True +2790 PIK3CA R975S False +3685 PTPRD R995C False +3429 ARHGAP35 R997* False +2925 PRPS1 S103I True +2926 PRPS1 S103N True +2927 PRPS1 S103T True +3497 ERBB2 S1050L False +2165 FANCA S1088F False +3647 KDR S1100F False +4333 ALK S1206R False +172 ALK S1206Y True +4130 TP53 S127Y False +3969 BRCA1 S1486C False +1499 PIK3CA S158L True +3964 BRCA1 S1655F False +3557 PTEN S170R False +3391 TP53 S183L False +4393 BRCA1 S1841N False +4394 BRCA1 S1841R False +2347 IL7R S185C False +1671 ROS1 S1986F False +1670 ROS1 S1986Y False +4290 MPL S204P False +10 ARAF S214C True +4410 ARAF S214F True +2715 MTOR S2215F False +542 MTOR S2215Y True +4472 ARAF S225V False +4143 TP53 S227C False +243 ATM S2289* True +1065 TP53 S241C False +2777 TP53 S241F True +3788 TP53 S241T True +628 FGFR3 S249C True +3674 NOTCH1 S2514A False +3676 NOTCH1 S2514E False +3677 NOTCH1 S2514P False +4312 SMAD2 S276L True +1562 SMO S278I False +3709 AR S296R False +2946 FGFR2 S320C False +3710 AR S334P False +3254 CTNNB1 S33F False +2281 CTNNB1 S37C False +1495 ABL1 S438C False +2615 EGFR S442I False +2614 EGFR S442R False +2897 NT5C2 S445F True +3502 ERCC2 S44L False +1832 POLE S459F True +1286 CTNNB1 S45F True +1287 CTNNB1 S45P True +692 ESR1 S463P True +2601 EGFR S464L False +2602 EGFR S464T False +825 ARAF S490T True +2610 EGFR S492C False +453 EGFR S492R True +1206 KIT S501_A502INSAY False +1589 SMO S533N False +1290 JAK3 S61C False +1659 KIT S628N True +4408 EGFR S645C True +2956 JAK1 S646F False +980 KIT S692L False +822 JAK1 S703I True +3680 JAK1 S729C False +891 EGFR S752_I759delSPKANKEI False +3723 AR S759P False +562 EGFR S768I True +1443 EGFR S768N False +145 DDR2 S768R True +1182 EGFR S784F False +2701 CBL S80N False +3347 SPOP S80R False +3750 ARHGAP35 S866F False +262 ABCB1 S893T True +3652 KDR S925F False +3645 PIM1 S97N True +4330 ALK T1151K False +1493 ALK T1151M False +743 MLH1 T117M True +3417 TP53 T125R False +3684 TP53 T125T True +3558 PTEN T160I False +4398 BRCA1 T1700A False +3979 BRCA1 T1720A False +2712 MTOR T1977K False +3412 MTOR T1977R False +540 FLT3 T227M True +3782 TP53 T230S True +1587 SMO T241M False +3675 NOTCH1 T2512A False +995 EGFR T263P True +901 ATM T2666A True +3629 BRCA2 T2722R False +3407 PTEN T277A False +3406 PTEN T277I False +3403 PTEN T277R False +2918 PRPS1 T303S True +2 ABL1 T315I True +870 BTK T316A True +2618 EGFR T415M False +1546 KIT T417_D419DELTYDINSI False +2620 KIT T417_D419delinsY True +1285 CTNNB1 T41A True +3503 ERCC2 T46S False +2795 BRAF T488_P492del False +974 KIT T574A False +3445 BRAF T598I False +2824 BRAF T599_V600insT False +2387 CSF3R T618I True +979 KIT T661I False +1267 KIT T670I True +861 EGFR T725M False +3686 PTPRD T781A False +1573 EGFR T785A True +34 EGFR T790M True +2331 ERBB2 T798I True +1305 ERBB2 T798M False +4321 NFE2L2 T80K False +1463 EGFR T847I True +1467 EGFR T854A False +871 ERBB2 T862A True +701 ERBB3 V104M True +528 ALK V1180L True +2624 TP53 V135A False +1254 TP53 V143A False +4411 ARAF V145L True +2991 KRAS V14I False +3968 BRCA1 V1534M False +2836 MAP2K1 V154I False +3059 BCL2 V156D False +1143 NOTCH1 V1577A False +1144 NOTCH1 V1577E False +3574 TP53 V157D False +1092 TP53 V157F True +1249 BRCA2 V159M True +3554 PTEN V166I False +3970 BRCA1 V1688del False +4399 BRCA1 V1713A False +4117 TP53 V173G False +1086 TP53 V173L False +4139 TP53 V173M False +3998 BRCA1 V1804D False +4396 BRCA1 V1838E False +3595 TP53 V197E False +4120 TP53 V197L False +2805 MAP2K1 V211D False +1251 BRCA2 V211I True +1250 BRCA2 V211L True +3507 ERCC2 V242F False +2348 IL7R V253G False +792 PTPRD V253I True +4123 TP53 V272G True +1035 TP53 V272L False +3790 TP53 V274F True +2751 TP53 V274S False +1604 ABL1 V289I False +2277 CRLF2 V2del False +1576 SMO V321M False +775 MSH6 V352I True +2841 MAP2K2 V35M False +2702 CBL V391I False +1831 POLE V411L True +2612 EGFR V441D False +2613 EGFR V441F True +2611 EGFR V441G False +745 MLH1 V49A True +728 MLH1 V534R True +2938 PRPS1 V53A True +3217 FGFR4 V550E False +2399 FGFR3 V555L False +2400 FGFR3 V555M True +1543 KIT V555_I571DEL False +957 KIT V555_P573DEL False +956 KIT V555_Q556DEL False +2695 KIT V555_V559DEL True +969 KIT V559A False +968 KIT V559D True +966 KIT V559DEL False +970 KIT V559G False +967 KIT V559_V560DEL False +971 KIT V560D True +202 KIT V560DEL True +972 KIT V560G True +1550 KIT V560_L576DEL True +247 PDGFRA V561A True +941 PDGFRA V561D True +2781 FGFR1 V561M False +1551 KIT V569_L576DEL False +1632 FLT3 V592_D593INSDFREY False +3446 BRAF V599E False +3453 BRAF V599K False +3454 BRAF V599R False +11 BRAF V600D True +3452 BRAF V600D False +12 BRAF V600E True +1199 BRAF V600G False +563 BRAF V600K True +1404 BRAF V600L False +1405 BRAF V600M True +16 BRAF V600R False +991 BRAF V600R False +1658 BRAF V600_K601DELINSD False +3241 BRAF V600_S605delinsDV False +2825 BRAF V601E False +2834 MAP2K1 V60E False +64 JAK2 V617F True +73 KIT V654A True +3205 PDGFRA V658A False +1289 JAK3 V722I False +3230 RET V738A False +1001 EGFR V742A True +3721 AR V757A False +3722 AR V757I False +1578 EGFR V769A False +736 EGFR V769_D770insASV True +872 ERBB2 V773A True +1311 ERBB2 V773L False +1892 EGFR V774A True +1894 EGFR V774M True +1567 EGFR V774_C775insHV False +44 ERBB2 V777L True +2568 RET V804M False +1897 EGFR V834I True +45 ERBB2 V842I True +1466 EGFR V851I True +781 ERBB3 V855A True +3668 PIK3CA V955G True +3001 PIK3CA V955I True +1521 CDKN2A W110* False +3691 PTPRB W130R False +1590 PTCH1 W170X False +3978 BRCA1 W1718C False +1555 BRCA1 W1815X True +3995 BRCA1 W1837R False +3627 BRCA2 W2626C False +1563 SMO W281C False +1583 SMO W281L False +2945 FGFR2 W290C False +4403 CDH1 W409R False +3688 ABL2 W469C False +2667 MPL W515L False +837 SMO W535L False +959 KIT W557G False +958 KIT W557R False +960 KIT W557T False +962 KIT W557_E561del False +961 KIT W557_K558del True +1498 KIT W557_V559insC False +1539 PDGFRA W559_R560DELWR False +1292 JAK1 W690* False +1591 PTCH1 W712X False +1571 EGFR W731L True +2703 CBL W802* False +3250 VHL W88* False +2913 MET Y1003H False +935 PIK3CA Y1021C False +3762 TP53 Y126D True +3763 TP53 Y126S True +3456 EP300 Y1414C False +3500 ERCC2 Y14C False +1645 PAPPA2 Y1520X False +1087 TP53 Y163C False +3769 TP53 Y163H True +3800 TP53 Y163N True +4395 BRCA1 Y1853C False +3506 ERCC2 Y209C False +922 TP53 Y220C True +3779 TP53 Y220H True +1596 ABL1 Y232S False +1068 TP53 Y234C True +3781 TP53 Y234H True +3770 TP53 Y236S True +3501 ERCC2 Y24C False +803 RUNX1 Y260* True +3614 BRCA2 Y2660D False +3609 BRCA2 Y2726C False +3690 PTPRB Y309C False +2934 PRPS1 Y311C False +3405 PTEN Y336* False +1605 ABL1 Y342H False +2377 RHEB Y35N False +2638 CBL Y371H True +2404 FGFR3 Y373C True +3356 FGFR2 Y375C False +3065 FGFR2 Y376C False +1611 ABL1 Y393C False +3689 ABL2 Y399C False +3239 KIT Y503A False +946 KIT Y503_F504insAY True +1669 LYN Y508F False +48 ESR1 Y537C True +49 ESR1 Y537N True +50 ESR1 Y537S True +952 KIT Y553D False +2737 KIT Y553N False +953 KIT Y553_K558DEL False +1542 KIT Y553_W557DELYEVQW False +1548 KIT Y570_L576DEL False +3233 FLT3 Y589D False +1630 FLT3 Y591_V592INSVDFREYE False +3607 EZH2 Y646C True +2989 EZH2 Y646F True +3364 EZH2 Y646H True +4090 EZH2 Y646N True +2666 EZH2 Y646S True +3514 FGFR3 Y647C False +2986 STAT5B Y665F False +3499 ERCC2 Y72C False +3606 EZH2 Y731D False +3724 AR Y763C False +1665 EGFR Y764_V765insHH True +1575 EGFR Y801H True +3228 RET Y806C False +3229 RET Y806N False +989 KIT Y823D True +3665 ERBB2 Y835F False +3070 FLT3 Y842C True +3234 FLT3 Y842H False +3535 PTEN Y88C False +1642 POLD1 Y956N False +3045 VHL p.F76del False +4475 MAP2K1 p.K57_G61del False +3310 HDAC9 p.L33R False +4474 BRAF p.N486_P490 False diff --git a/analysis/civic/unable_to_normalize_queries.csv b/analysis/civic/unable_to_normalize_queries.csv new file mode 100644 index 0000000..25bb1ad --- /dev/null +++ b/analysis/civic/unable_to_normalize_queries.csv @@ -0,0 +1,64 @@ +variant_id query query_type variant_accepted exception_raised message warnings +748 MLH1 *757L protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3718 AR A748V protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3725 AR A765T protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +248 TERT C228T protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +4004 TERT C250T protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3706 AR D221H protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3713 AR D528G protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2833 NECTIN4 D594H protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2514 3-10183806-A-CC genomic False False unable to normalize ['Unable to find valid result for classifications: set()'] +3707 AR E198G protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +4420 HBB E6V protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +457 FCGR3A F212V protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3450 BRAF F594L protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3793 TP53 G177E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3152 GNA11 G209P protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3153 GNAQ G209P protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3443 BRAF G465A protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3441 BRAF G468A protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +4298 FGFR3 G802_X807del protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein deletion'}""]" +3448 BRAF I462S protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2137 3-10191481-GAA-C genomic True False unable to normalize ['Unable to find valid result for classifications: set()'] +3023 PML K227_T233del protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein deletion'}""]" +2815 H3C2 K27M protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3939 H3-3A K27M protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3944 H3C14 K27M protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3594 H3-3A K27R protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2420 H3-3B K36M protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2696 KIT K550_K559DEL protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein deletion'}""]" +3455 BRAF K600E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3714 AR K720E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +4114 TP53 L139N protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +424 MYD88 L265P protein True False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +1540 PDGFRA L579M protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +1309 ERBB2 L638S protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3717 AR L744F protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3435 MYOD1 MYOD1 L122R protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3719 AR N756D protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3711 AR P340L protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3712 AR P504L protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +1643 SCN8A Q225X protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2700 CBL Q294E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3726 AR Q798E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +1975 3-10191506-CGGAGC-T genomic False False unable to normalize ['Unable to find valid result for classifications: set()'] +3069 NTRK3 R248C protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3447 BRAF R461I protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3716 AR R726L protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3674 NOTCH1 S2514A protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3676 NOTCH1 S2514E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3677 NOTCH1 S2514P protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3709 AR S296R protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3723 AR S759P protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3675 NOTCH1 T2512A protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +1546 KIT T417_D419DELTYDINSI protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein deletion'}""]" +3445 BRAF T598I protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2624 TP53 V135A protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3446 BRAF V599E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3453 BRAF V599K protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3454 BRAF V599R protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +2825 BRAF V601E protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3721 AR V757A protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3722 AR V757I protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +3724 AR Y763C protein False False unable to normalize "[""Unable to find valid result for classifications: {'protein substitution'}""]" +4474 BRAF p.N486_P490 protein False False unable to normalize ['Unable to tokenize p.N486_P490'] diff --git a/analysis/moa/able_to_normalize_queries.csv b/analysis/moa/able_to_normalize_queries.csv new file mode 100644 index 0000000..31f4106 --- /dev/null +++ b/analysis/moa/able_to_normalize_queries.csv @@ -0,0 +1,180 @@ +variant_id query moa_feature_type category vrs_id +71 ABL1 p.T315I somatic_variant Protein Consequence ga4gh:VA.M3CbaYfwomLqvJbdK4w-W7V-zw7LdjGj +73 ABL1 p.T315A somatic_variant Protein Consequence ga4gh:VA.Z9Ygies0W47sv7z1LXuMrD8ql6eFv_Fb +75 ABL1 p.F317L somatic_variant Protein Consequence ga4gh:VA.KthZ0GvMM8IAq73dQ1Bqh9e8Ys0LKL8p +76 ABL1 p.F317V somatic_variant Protein Consequence ga4gh:VA.ZQYG0E49jxi2VTHK3Fmfktzg5KBW0is5 +77 ABL1 p.F317I somatic_variant Protein Consequence ga4gh:VA.KNp3-VqwztR6vlk9k4x1XhebBhFX3nFe +78 ABL1 p.F317C somatic_variant Protein Consequence ga4gh:VA.yabDtFWLSKupTecNEMcVNAz9cfqKp6zN +80 ABL1 p.E255K somatic_variant Protein Consequence ga4gh:VA.egYObxBPDqf6cCMPijlIZ0QyLPa3-wO7 +81 ABL1 p.E255V somatic_variant Protein Consequence ga4gh:VA.9pODtea47dZXXpsMJ667fBidWbvshZS2 +82 ABL1 p.Y253H somatic_variant Protein Consequence ga4gh:VA.R14JDsYJaw2AXsnZnsryvMsWDm3QHZDI +83 ABL1 p.F359V somatic_variant Protein Consequence ga4gh:VA.hjWYzEi6IM-mGx_QsWNNrBLTQEClE3S3 +84 ABL1 p.F359C somatic_variant Protein Consequence ga4gh:VA.Pd684Wlp6DAMMDYWF9O4aAMvrpA25ydF +85 ABL1 p.F359I somatic_variant Protein Consequence ga4gh:VA.lFh0aJl2ac78dIMyomiZGrDyCz6hA_U1 +97 ABL1 p.V299L somatic_variant Protein Consequence ga4gh:VA.sBWM34QhP2rjVTFWajgauhJ3QeN61TxY +108 ABL1 p.T315I somatic_variant Protein Consequence ga4gh:VA.M3CbaYfwomLqvJbdK4w-W7V-zw7LdjGj +112 AKT1 p.E17K somatic_variant Protein Consequence ga4gh:VA.ulPeadFf5rMg7tG-WFIvGOPgFBgFBmvm +115 ALK p.G1202R somatic_variant Protein Consequence ga4gh:VA.otN-O6TmlrfPGEU-YDDmtdaXLY7zk4Zc +116 ALK p.F1174C somatic_variant Protein Consequence ga4gh:VA.QtaGjdrAZEW4sT-7WAwaCwYghSEdhh8s +117 ALK p.L1196M somatic_variant Protein Consequence ga4gh:VA.rdhnlJk8MzBxdYL4tHC4gHvUyciQw6KW +118 ALK p.G1269A somatic_variant Protein Consequence ga4gh:VA.FuEnPmOTyaN9jQNc1qML9_A5FT64KZAF +119 ALK p.S1206Y somatic_variant Protein Consequence ga4gh:VA.3zaL4c_h9jsZJmXjCeO1he6URh1D0rqs +120 AR p.T878A somatic_variant Protein Consequence ga4gh:VA.92QuivGuiyqCJsmqOnbFNZfrQUC6eOf2 +121 AR p.L702H somatic_variant Protein Consequence ga4gh:VA.jLpXngL9t3ngVDCusTkj6FLkCK_QT3lu +122 ARAF p.S214C somatic_variant Protein Consequence ga4gh:VA.thaNPIsobhJxAwkWJ_0BALvT2XyOo6mj +134 ATM p.A1127D somatic_variant Protein Consequence ga4gh:VA.AslIv3xIzYDTc175EDYbFjHvYbZuwCf2 +146 BCOR p.N1425S somatic_variant Protein Consequence ga4gh:VA.RnYeelgIkUGa8EveljO5dJOA-ag6CJkE +149 BRAF p.V600E somatic_variant Protein Consequence ga4gh:VA.ZDdoQdURgO2Daj2NxLj4pcDnjiiAsfbO +151 BRAF p.V600K somatic_variant Protein Consequence ga4gh:VA.EReJZvr-VBO8123VDpv4Gvg0jvLZh_gH +250 DNMT3A p.R882H somatic_variant Protein Consequence ga4gh:VA.EPhBezYC3g3EoxzsMN_xcmt4-YZgSwkc +254 EGFR p.T790M somatic_variant Protein Consequence ga4gh:VA.BldHTcxmxpKf1exsSbeuki1jhdek1GaJ +267 EGFR p.L858R somatic_variant Protein Consequence ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA +284 EGFR p.L858R somatic_variant Protein Consequence ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA +286 EGFR p.L858R somatic_variant Protein Consequence ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA +294 ERRFI1 p.E384* somatic_variant Protein Consequence ga4gh:VA.SfZhr3jxZr_-mGixUD0HDQwQIoirkBCB +300 EZH2 p.Y646* somatic_variant Protein Consequence ga4gh:VA.AmHnsLSTJCx_-X2xBhyx9HmhY8kn3iy4 +301 EZH2 p.Y646F somatic_variant Protein Consequence ga4gh:VA.fIFZFyzJRiGTt2CRRD2DUSSQ_1cA2dDi +302 EZH2 p.Y646N somatic_variant Protein Consequence ga4gh:VA.zjbm34xh4ZI54ihvCj8XA-nZQMdSF97I +303 EZH2 p.A682G somatic_variant Protein Consequence ga4gh:VA.BMvnGn1upgP_4DhUZzqq7nTrBZeGwlgM +304 EZH2 p.A692V somatic_variant Protein Consequence ga4gh:VA.tHiuDXC6Tt9d5I2QSfMA3oPqwFojDoBp +307 FGFR3 p.R248C somatic_variant Protein Consequence ga4gh:VA.Ef_9GdbuoBbTePILS-NaQJn-_NhrdpoO +308 FGFR3 p.S249C somatic_variant Protein Consequence ga4gh:VA.g3wMkTfExru4z6L-cpP5OgujLJyvQQfV +309 FGFR3 p.G370C somatic_variant Protein Consequence ga4gh:VA.F19w5rQJOPFV5ratrP1qhkNUUEk8l7Ee +310 FGFR3 p.Y373C somatic_variant Protein Consequence ga4gh:VA.Te_5eCSBPCF7A2FyyGRQ5n_86SWBUomZ +317 FLT3 p.F691L somatic_variant Protein Consequence ga4gh:VA.4_yATGhcl_NWTFAxlYcxqJ5JTHfSzaRO +318 FLT3 p.K663Q somatic_variant Protein Consequence ga4gh:VA.FMnRMOr3rTGVayWvCfBuep9v7Hdu2IVT +319 GATA3 p.M294K somatic_variant Protein Consequence ga4gh:VA.CILcwMmLL6e0GYyvF0I70t06hNWj5iGB +323 IDH1 p.R132H somatic_variant Protein Consequence ga4gh:VA.iZh-igOaUaWlGiz1m3WbZUVvwDyLEJ4R +324 IDH1 p.R132C somatic_variant Protein Consequence ga4gh:VA.O8zC-ad_EKRCy_aO0XPs5spF0sEYDsU0 +329 IDH2 p.R140Q somatic_variant Protein Consequence ga4gh:VA.RNA3TdZTniFNEIgKSLqiNm4LE9JE2Xwb +330 IDH2 p.R172S somatic_variant Protein Consequence ga4gh:VA.VV9OqRgs_36WZlVj6nlsXQmHSjV7uvL0 +331 IDH2 p.R172K somatic_variant Protein Consequence ga4gh:VA.FRHhQf23W6IpLwB95kjW5e_3QRmJzaG2 +334 IDH2 p.R140Q somatic_variant Protein Consequence ga4gh:VA.RNA3TdZTniFNEIgKSLqiNm4LE9JE2Xwb +338 JAK1 p.V656F somatic_variant Protein Consequence ga4gh:VA.V2isIxZY6ZV2-100-DvNakriSprlomGe +339 JAK1 p.A634D somatic_variant Protein Consequence ga4gh:VA.HjfGS4usbLzdIuhmo-30l-telWZY6CzG +341 JAK2 p.V617F somatic_variant Protein Consequence ga4gh:VA.JiaDMZmDvTa7T_zVcVX8UWf4x9X6jG3_ +342 JAK3 p.A572T somatic_variant Protein Consequence ga4gh:VA.crmrR_XiXSwPKJmnQS-OQoPWXsRMJkh- +343 JAK3 p.M511I somatic_variant Protein Consequence ga4gh:VA.qd7dq7ybsIeDC4f6GJo3bZxOruexl4li +344 JAK3 p.L857Q somatic_variant Protein Consequence ga4gh:VA.i1VOJJgI77GHg9liTOl7ZSv80kOl3Ce7 +352 KIT p.T670I somatic_variant Protein Consequence ga4gh:VA._L7r4YO_nW3etQySFzjREsHI4j4qnzPv +353 KIT p.V654A somatic_variant Protein Consequence ga4gh:VA.2jbEOWQLfQD0H3qVUZbVKlzA1EBhvA41 +361 KIT p.W557C somatic_variant Protein Consequence ga4gh:VA.Bh11Y4LpqNgI7KB0GYplBjb2Aiv2OxBb +362 KIT p.W557G somatic_variant Protein Consequence ga4gh:VA.-X5LgVajv8hJeieqJbBFI6PnjHgyUtIH +363 KIT p.W557R somatic_variant Protein Consequence ga4gh:VA.bJNRtqyXrTpZxrFJmZ6yzOhGrDGY-4-S +364 KIT p.V559A somatic_variant Protein Consequence ga4gh:VA.nPBn1g_GPr7nSNOcDBor9pLGJsyZZZoX +365 KIT p.V559G somatic_variant Protein Consequence ga4gh:VA.rdmWjmfv5r1vV2x97NdpqzKodyj5DMPp +366 KIT p.L576P somatic_variant Protein Consequence ga4gh:VA.z2MmOn-EKde3j5N0335DbKXvMRHZ8sfg +367 KIT p.K642E somatic_variant Protein Consequence ga4gh:VA._9KiRvPkoZgN3sRLRN28HKM0uQ1Ndq5- +369 KIT p.D816H somatic_variant Protein Consequence ga4gh:VA.vHPfPMGRksMr4zLq-aO7BKHeBS5GoEle +374 KIT p.D816V somatic_variant Protein Consequence ga4gh:VA.QSLb0bR-CRIFfKIENdHhcuUZwW3IS1aP +387 KRAS p.G12C somatic_variant Protein Consequence ga4gh:VA.GtaY-fkmnMXM-bRKyu5qvya6Zd47AM_X +390 KRAS p.G12D somatic_variant Protein Consequence ga4gh:VA.NtQTqsdO_Z8G0KpBQ1_z7QsHo_bVN43m +402 MAP2K1 p.P124L somatic_variant Protein Consequence ga4gh:VA.Uhggl0kfMZ_MaFNo57-aSkvjs3BtjdGj +403 MAP2K1 p.Q56P somatic_variant Protein Consequence ga4gh:VA.Tkb5vESjzbd7eUDOsmfUlhmg-TJTQM7g +408 MAP2K1 p.C121S somatic_variant Protein Consequence ga4gh:VA.wjBDXOXnaZTkYjuhTe0Ey9RQIVS6XIfh +410 MAP2K2 p.Q60P somatic_variant Protein Consequence ga4gh:VA.JU8Hqa9UAwea5fKWJJf_Ou757cz570rz +411 MAPK1 p.E322K somatic_variant Protein Consequence ga4gh:VA.gd71aR16HOc7-nHLRgykfj7LcOyu6BFA +413 MET p.T1010I somatic_variant Protein Consequence ga4gh:VA.J5zBAhB6Tps4S-IsqGNV0azxeW6rH-BP +421 MPL p.W515L somatic_variant Protein Consequence ga4gh:VA.ONjwKW5tR0w95SbU5EUCfuPIvQxhWtdN +432 NRAS p.G12A somatic_variant Protein Consequence ga4gh:VA.078FsMCLsPQusaDNRNcE9iCuk52ffs0_ +433 NRAS p.G12C somatic_variant Protein Consequence ga4gh:VA.gb0-lfGQqY52tTY-gQNkpQk_-kjOUMBh +434 NRAS p.G12D somatic_variant Protein Consequence ga4gh:VA.6fySa8P47Q7DjsqrGKMSKS2fYpzdZdl3 +435 NRAS p.G12R somatic_variant Protein Consequence ga4gh:VA.q73ZQ79FDV0K53ZWebb4Z4MIb0SK9ros +436 NRAS p.G12S somatic_variant Protein Consequence ga4gh:VA.DJ3mHANAwaWBHoP_tlAABMVJOpbi43Wt +437 NRAS p.G12V somatic_variant Protein Consequence ga4gh:VA.5Jmah15DhleqR_L4Cceck2zoYY4UAckz +438 NRAS p.G13A somatic_variant Protein Consequence ga4gh:VA.K8aKwv4QxelxHWPk9N1yMw8Zx0osv-LO +439 NRAS p.G13D somatic_variant Protein Consequence ga4gh:VA.Vi9_O1D0NZjlJHY1C8iErs1ulF2NLy0f +440 NRAS p.G13R somatic_variant Protein Consequence ga4gh:VA.4tkCjhl90tVBA3W8-4kPbKjOp82X16yp +441 NRAS p.G13V somatic_variant Protein Consequence ga4gh:VA.1_DTGp3bCIrFFYD-jhIYggCZRvhFY9P9 +442 NRAS p.Q61E somatic_variant Protein Consequence ga4gh:VA.4MnG-a7SvcUvkG9n_UWR189DHx97PJj_ +443 NRAS p.Q61H somatic_variant Protein Consequence ga4gh:VA.qPk_A1ivYE7HIKO5GasYeFbzPT_w6drG +444 NRAS p.Q61L somatic_variant Protein Consequence ga4gh:VA.5O7aEDzcl7FhKsqeg5WT_iirqIjCpHTr +446 NRAS p.Q61P somatic_variant Protein Consequence ga4gh:VA.kXUi5jG-vEQvI1M68QnNiCsgECWC1H0- +447 NRAS p.Q61R somatic_variant Protein Consequence ga4gh:VA.UtLI1rrsdnYpKO9B6xHJBsUHmJ6tRrYn +459 PDGFRA p.D842V somatic_variant Protein Consequence ga4gh:VA.bjWVYvXPaPbIRAfZvE0Uw_P-i36PGkAz +467 PIK3CA p.E545Q somatic_variant Protein Consequence ga4gh:VA.I2EHsdyKa1RU5mQCVuLxQNcqUODKbmaW +468 PIK3CA p.C420R somatic_variant Protein Consequence ga4gh:VA.Nxz0N4ov2iqketOQz74Sipp8LgXVyoux +469 PIK3CA p.E542K somatic_variant Protein Consequence ga4gh:VA.fH_NA-yLHTsF_P_SRqWYD-SYe8kIP2IX +470 PIK3CA p.E542Q somatic_variant Protein Consequence ga4gh:VA.2OmWkE5p_GQ9GqfWDHXPMsQdUwinH9Ro +471 PIK3CA p.E545A somatic_variant Protein Consequence ga4gh:VA.cHMY4gTf2MB-43xJURhOJNZERiGzvQYH +472 PIK3CA p.E545D somatic_variant Protein Consequence ga4gh:VA.R1KBKRC-bkw7EThjVXgYKYcJkVBxUihR +474 PIK3CA p.E545G somatic_variant Protein Consequence ga4gh:VA.WABk-_bU9ObST0H0eE72hIj0OEpX78eY +475 PIK3CA p.E545K somatic_variant Protein Consequence ga4gh:VA.JtbA5ylDOt1lGLvvYwybn_s_-vLB8cvh +476 PIK3CA p.G1049R somatic_variant Protein Consequence ga4gh:VA.wodcxMzUiTgouTS4hF7Eds_L-EDI5UaC +477 PIK3CA p.G1049S somatic_variant Protein Consequence ga4gh:VA.zjfgoWCV21ThRUo54z4iBB5djQuJuERi +478 PIK3CA p.H1047L somatic_variant Protein Consequence ga4gh:VA.VkzlYLUG-zVXR5dU-rz4Y3I_twI3kUVs +479 PIK3CA p.H1047R somatic_variant Protein Consequence ga4gh:VA.RlhlEsuf37TD4nAC2ECL6onq-8AG80mw +480 PIK3CA p.H1047Y somatic_variant Protein Consequence ga4gh:VA.Z1QMZdtOXAu2up3amTCzusY8jOkko0SQ +481 PIK3CA p.H701P somatic_variant Protein Consequence ga4gh:VA.NBIOXXLLxiLvmmnDI4BiJtLXQWjCZneS +482 PIK3CA p.M1043I somatic_variant Protein Consequence ga4gh:VA.TdExGXHZflky6uB4RxkWLqDeUWSTeH59 +484 PIK3CA p.P539R somatic_variant Protein Consequence ga4gh:VA._hllTuMEA7f9kETf1jW4TmsSOkpp5OL1 +485 PIK3CA p.Q546K somatic_variant Protein Consequence ga4gh:VA._TDbkBGDlBX6EfTuxt2Jv-9QUXwEQzUv +486 PIK3CA p.Y1021C somatic_variant Protein Consequence ga4gh:VA.etF8HNjm7urbqzQfnzw-7FuGnaUpghip +488 POLD1 p.D316H somatic_variant Protein Consequence ga4gh:VA.lgfMkuCVMWuD-GRLkMSNo8sfLnVjOYQe +489 POLD1 p.D316G somatic_variant Protein Consequence ga4gh:VA.rL_qODeSKGKfu81wq5_RPsnUVY2WJ458 +490 POLD1 p.R409W somatic_variant Protein Consequence ga4gh:VA.9xm45KgAF4IP1_UzH749OWSixS96CBpC +491 POLD1 p.L474P somatic_variant Protein Consequence ga4gh:VA.81ePQcwIoV7ns3TM7DCqwhLJzNa1C1Ar +495 POLE p.L424V somatic_variant Protein Consequence ga4gh:VA.lN1M09gvpGPkL4elvta2DbATRC2akF8y +529 RET p.V804M somatic_variant Protein Consequence ga4gh:VA.i3Wijz4w7QwMom0qmvd-DYEU2WPWDuIP +530 RET p.M918T somatic_variant Protein Consequence ga4gh:VA.GweduWrfxV58YnSvUBfHPGOA-KCH_iIl +535 SETBP1 p.E858K somatic_variant Protein Consequence ga4gh:VA.zFFngSUVJ67HaDGFyYq-5GSMjVvFtoWA +536 SETBP1 p.T864M somatic_variant Protein Consequence ga4gh:VA.5XU0aGLWrdDTqnyeptt6gt2Z5J1wIszf +538 SETBP1 p.D868N somatic_variant Protein Consequence ga4gh:VA.4pM7_VkkVJ2H06gTP9haIh57dOYgD5mT +539 SETBP1 p.D868Y somatic_variant Protein Consequence ga4gh:VA.o28LVBUPirbBW6oLfh940Ggo3s9ML11X +540 SETBP1 p.S869C somatic_variant Protein Consequence ga4gh:VA.HTY8eskMSTD6cCxzHyJumXBOH2ye01Ok +541 SETBP1 p.G870S somatic_variant Protein Consequence ga4gh:VA.PeKwQARIuzTLu2IfearnmVqdQ324sAnS +543 SF3B1 p.E622Q somatic_variant Protein Consequence ga4gh:VA.8NQehrkhe8JGaf0u92j5aFq9yZpdFl3G +544 SF3B1 p.E622D somatic_variant Protein Consequence ga4gh:VA.MXUqXc80HWqWjSEMUoKwyz8ieeFWhdEF +545 SF3B1 p.Y623C somatic_variant Protein Consequence ga4gh:VA.zwD01W295y5y1_eeOhsOfW1PCUH0D9Tb +546 SF3B1 p.R625C somatic_variant Protein Consequence ga4gh:VA.uxmbcPMjgDJ7JTCXuAv-QQis5elwK6V7 +547 SF3B1 p.R625H somatic_variant Protein Consequence ga4gh:VA.DKiDwvrdV0VlYyLfX1NG3rXRkbpW4xPo +548 SF3B1 p.N626H somatic_variant Protein Consequence ga4gh:VA.S_qr-JKNuboc_SJKFTzuWq12BClLJzNG +549 SF3B1 p.N626Y somatic_variant Protein Consequence ga4gh:VA.X_11i7OBao6O0lUNPmzBDo2eW7rx08Ci +550 SF3B1 p.N626D somatic_variant Protein Consequence ga4gh:VA.nE_DhEarl40lgTYDD-2yKRZXCc5U4nkH +551 SF3B1 p.H662R somatic_variant Protein Consequence ga4gh:VA.IH1ZOBNFeQz_fSe_LMnbwKXPd70oatyd +552 SF3B1 p.T663P somatic_variant Protein Consequence ga4gh:VA.IJxOQXdNwWyM1tmZ6NdBrIsU9XcxHHHw +553 SF3B1 p.K666N somatic_variant Protein Consequence ga4gh:VA.9-Y2ZQvL5kCe0GLuveRxI9yUovIu2nyp +554 SF3B1 p.K666T somatic_variant Protein Consequence ga4gh:VA.5c3U7EZPFQl3gdxKeMXiho3SdINNy6PQ +555 SF3B1 p.K666E somatic_variant Protein Consequence ga4gh:VA.9g43GsUYgSrLkkr5l9A_NQn3IxTWeUmK +556 SF3B1 p.K700E somatic_variant Protein Consequence ga4gh:VA.whO8Hvl7PXuKA_tJf4Iy7VeyU-aWfFNT +558 SF3B1 p.G740E somatic_variant Protein Consequence ga4gh:VA.gxstydORFgAtfgAsP385BpHrKEaZ2SzQ +559 SF3B1 p.G740V somatic_variant Protein Consequence ga4gh:VA.EdObQ12d63WVDCd1ReKihBSDtq0mSa92 +560 SF3B1 p.G742D somatic_variant Protein Consequence ga4gh:VA.E-PTd0OMD4XYok50BVfrY7QyzKYzOMbK +561 SF3B1 p.D781E somatic_variant Protein Consequence ga4gh:VA.MGqDRndHFa22Kigl6mqte5iYPfNBkvZr +654 IL12RB1 p.Q32* germline_variant Protein Consequence ga4gh:VA.SeRUlUdAJjHAitGJLijohmdGBJftazH3 +655 IL12RB1 p.Q542* germline_variant Protein Consequence ga4gh:VA.CsBzsgPC15Bn2QEKWbrnRX4ejGWLffXM +661 MRE11 p.R576* germline_variant Protein Consequence ga4gh:VA.bSNc2R2mVCuudfIlJf6TQ4U1y08-InaN +680 POT1 p.R363* germline_variant Protein Consequence ga4gh:VA.fsScHMChEdKitMrP_ZmBwg2G1uKA5_zi +696 AR Amplification copy_number Copy Number ga4gh:CX.VIJD6vu8rhtcw-preGLm1j3GOJ15s8nc +701 AURKA Amplification copy_number Copy Number ga4gh:CX.uLiJZi49tL7UJtcC8qmt0dXigJLG17AW +703 AURKB Amplification copy_number Copy Number ga4gh:CX.LiOYJ5mIepwd7OoWzYvPTNoAyL19QHWN +704 BRAF Amplification copy_number Copy Number ga4gh:CX.TZBOQe5xFojvFJ1XjQQD0633rStHtGUs +707 CCND1 Amplification copy_number Copy Number ga4gh:CX.juMpRJTQe-cXd5NwCZLkW4rYlSF3Wy0r +708 CCND1 Amplification copy_number Copy Number ga4gh:CX.juMpRJTQe-cXd5NwCZLkW4rYlSF3Wy0r +709 CCNE1 Amplification copy_number Copy Number ga4gh:CX.V9Dwgo088Y2XOdhS1NYQgsMFj48ApJKb +710 CD274 Amplification copy_number Copy Number ga4gh:CX.w0PrNyAG-TMPenT0y89L4KYjhKvMWoyq +716 CDK4 Amplification copy_number Copy Number ga4gh:CX.ms7wmVsTZc_x0cpgfDQFvplp8ptIHBH9 +724 CRKL Amplification copy_number Copy Number ga4gh:CX.co0a3VJT3K1f2Yo9PV_45vJfCM9j22p9 +725 EGFR Amplification copy_number Copy Number ga4gh:CX.sEHT64Lm86QaTXzw39uKLkBUbEkp4h_X +726 ERBB2 Amplification copy_number Copy Number ga4gh:CX.sfdL4tI7NYIKXtcL2jJyo3tzeoeYOOcS +744 ESR1 Amplification copy_number Copy Number ga4gh:CX.umsb1R9tid2EeT3JNFHgcMbbvxyB9AKr +746 FGFR1 Amplification copy_number Copy Number ga4gh:CX.H2AKyhB78TWf738tf7xGCXiqTN35A4fF +750 FGFR2 Amplification copy_number Copy Number ga4gh:CX.cd2wF23PpDn8-Y3HxFAhYi4hRBkxrx7e +754 HIF1a Amplification copy_number Copy Number ga4gh:CX.wylIQHINjN8vb7U3AcRwWhGz98KxS7QW +756 KIT Amplification copy_number Copy Number ga4gh:CX.TEy03PVyUmjHBTxanGyWzVMp20MHyio2 +757 MDM2 Amplification copy_number Copy Number ga4gh:CX.pVj4Qo53bz9VqFkyHuzH-MdahZnLwKIG +758 MET Amplification copy_number Copy Number ga4gh:CX.yUMibVYKc6dUxE982VhjXK-exeJydtQh +762 MIR17HG Amplification copy_number Copy Number ga4gh:CX.nYHmBCnU83iiMlywuEpF_sjnwEt1XuO9 +764 MRE11 Amplification copy_number Copy Number ga4gh:CX.Dm15EUtMB9BwDnYF3HkqoAWrHcPbyfbY +765 MYC Amplification copy_number Copy Number ga4gh:CX.dtGMpye8n2iy2Ly5SzUrzguxuVtflgST +766 MYC Amplification copy_number Copy Number ga4gh:CX.dtGMpye8n2iy2Ly5SzUrzguxuVtflgST +767 PAK1 Amplification copy_number Copy Number ga4gh:CX.7JflBccSlSdqQR2SHSRbzjdwaPYAUEdq +770 PIK3CA Amplification copy_number Copy Number ga4gh:CX.lLfUpR9E3ehVCteToRHhWUuRiePR0I7e +780 TPX2 Amplification copy_number Copy Number ga4gh:CX.mYdl9j8nh9kZKnmiyGgzX_oxn0EtTR_7 +854 MAP2K4 Amplification copy_number Copy Number ga4gh:CX.WLHYftcZOmFlGRrAC-tBoTdNRUieb5JG +857 MAPK7 Amplification copy_number Copy Number ga4gh:CX.RuiJ4Gam5-Oz1OugoMar16cjVaJfSBvF +858 MYOCD Amplification copy_number Copy Number ga4gh:CX.tMvgk273y1Gjt0GIj5GRxvSRb3UqsI84 +859 PDGFRA Amplification copy_number Copy Number ga4gh:CX.djhRFuSjFfI6vLoBQjIPD4krb7Unxkvu +868 IDH1 p.R132G somatic_variant Protein Consequence ga4gh:VA.nB9f7uL9HBJj70ZqSimBFCEwv_1W0KMC +869 IDH1 p.R132S somatic_variant Protein Consequence ga4gh:VA.jNPuoVr44MWaWXmffeUgLdN9lxYisgaa +870 IDH1 p.R132L somatic_variant Protein Consequence ga4gh:VA.My7Dz91of1BesZ9PVk5u_vovguNywRCr diff --git a/analysis/moa/moa_analysis.ipynb b/analysis/moa/moa_analysis.ipynb new file mode 100644 index 0000000..af9249f --- /dev/null +++ b/analysis/moa/moa_analysis.ipynb @@ -0,0 +1,805 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/kxk102/.local/share/virtualenvs/variation-normalization-KPVKcmjd/lib/python3.11/site-packages/python_jsonschema_objects/__init__.py:49: UserWarning: Schema version http://json-schema.org/draft-07/schema not recognized. Some keywords and features may not be supported.\n", + " warnings.warn(\n" + ] + } + ], + "source": [ + "from enum import Enum\n", + "import re\n", + "import csv\n", + "\n", + "from dotenv import load_dotenv\n", + "import requests\n", + "\n", + "from variation.query import QueryHandler" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Environment variables are set for gene-normalizer dynamodb instance and \n", + "# UTA DB credentials\n", + "load_dotenv()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "query_handler = QueryHandler()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "# Get all variants from MOA\n", + "r = requests.get(\"https://moalmanac.org/api/features\")\n", + "variants_resp = r.json()\n", + "variants = list()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "class VariantCategory(str, Enum):\n", + " \"\"\"Create enum for the kind of variants that are in MOA.\"\"\"\n", + " EXPRESSION = \"Expression\"\n", + " EPIGENETIC_MODIFICATION = \"Epigenetic Modification\"\n", + " FUSION = \"Fusion\"\n", + " PROTEIN_CONS = \"Protein Consequence\"\n", + " GENE_FUNC = \"Gene Function\"\n", + " REARRANGEMENTS = \"Rearrangements\"\n", + " COPY_NUMBER = \"Copy Number\"\n", + " OTHER = \"Other\"\n", + " GENOTYPES_EASY = \"Genotypes Easy\"\n", + " GENOTYPES_COMPOUND = \"Genotypes Compound\"\n", + " REGION_DEFINED_VAR = \"Region Defined Variant\"\n", + " INCOMPLETE_VAR = \"Incomplete Variants\"\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "# Map MOA Feature Type to Categories\n", + "moa_ft_to_variant_categories = {\n", + " \"rearrangement\": VariantCategory.REARRANGEMENTS,\n", + " \"somatic_variant\": VariantCategory.PROTEIN_CONS,\n", + " \"germline_variant\": VariantCategory.PROTEIN_CONS,\n", + " \"copy_number\": VariantCategory.COPY_NUMBER,\n", + " \"microsatellite_stability\": VariantCategory.REARRANGEMENTS,\n", + " \"mutational_signature\": VariantCategory.OTHER,\n", + " \"mutational_burden\": VariantCategory.OTHER,\n", + " \"neoantigen_burden\": VariantCategory.EXPRESSION,\n", + " \"knockdown\": VariantCategory.EXPRESSION,\n", + " \"silencing\": VariantCategory.EXPRESSION,\n", + " \"aneuploidy\": VariantCategory.COPY_NUMBER\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "# This file contains MOA Variants where there are no queries available. \n", + "no_query_wf = open(\"no_query.csv\", \"w\")\n", + "no_query_wr = csv.writer(no_query_wf, delimiter=\"\\t\")\n", + "no_query_wr.writerow([\"variant_id\", \"feature\"])\n", + "\n", + "# This file contains all queries we SHOULD be able to normalize\n", + "all_queries_wf = open(\"should_be_able_to_normalize_queries.csv\", \"w\")\n", + "all_queries_wr = csv.writer(all_queries_wf, delimiter=\"\\t\")\n", + "all_queries_wr.writerow([\"variant_id\", \"query\", \"moa_feature_type\", \"category\"])\n", + "\n", + "# This file contains MOAlmanac Variants we do not currently support in Variation Normalizer.\n", + "# In these cases, we do not even attempt to try to normalize\n", + "not_supported_wf = open(\"not_supported_variants.csv\", \"w\")\n", + "not_supported_wr = csv.writer(not_supported_wf, delimiter=\"\\t\")\n", + "not_supported_wr.writerow([\"variant_id\", \"query\", \"moa_feature_type\", \"category\"])\n", + "\n", + "# This file contains MOAlmanac Variant queries that we were not able to normalize.\n", + "unable_to_normalize_wf = open(\"unable_to_normalize_queries.csv\", \"w\")\n", + "unable_to_normalize_wr = csv.writer(unable_to_normalize_wf, delimiter=\"\\t\")\n", + "unable_to_normalize_wr.writerow([\"variant_id\", \"query\", \"moa_feature_type\", \"category\",\n", + " \"exception_raised\", \"message\", \"warnings\"])\n", + "\n", + "# This file contains MOAlmanac Variant queries that we were able to normalize.\n", + "able_to_normalize_wf = open(\"able_to_normalize_queries.csv\", \"w\")\n", + "able_to_normalize_wr = csv.writer(able_to_normalize_wf, delimiter=\"\\t\")\n", + "able_to_normalize_wr.writerow([\"variant_id\", \"query\", \"moa_feature_type\", \"category\",\n", + " \"vrs_id\"])\n", + "\n", + "# Category name for variants we do not support: number of variants we found\n", + "not_supported_feature_counts = {c: 0 for c in VariantCategory.__members__}\n", + "\n", + "# Keep track of total counts\n", + "total_variants = 0\n", + "no_query_total = 0\n", + "should_be_able_to_normalize_total = 0\n", + "can_normalize_total = 0\n", + "unable_to_normalize_total = 0\n", + "exception_total = 0\n", + "\n", + "for v in variants_resp:\n", + " total_variants += 1\n", + " variant_id = v[\"feature_id\"]\n", + " variant_record = {\n", + " \"id\": variant_id\n", + " }\n", + " variant_record.update(v[\"attributes\"][0])\n", + "\n", + " feature_type = variant_record[\"feature_type\"]\n", + " supported = False\n", + "\n", + " feature = None\n", + " if feature_type == \"rearrangement\":\n", + " feature = \"{}{}{}{}\".format(variant_record[\"gene1\"] if variant_record.get(\"gene1\") else \"\",\n", + " f\"--{variant_record['gene2']}\" if variant_record.get(\"gene2\") else \"\",\n", + " f\" {variant_record['locus']}\" if variant_record.get(\"locus\") else \"\",\n", + " f\" {variant_record['rearrangement_type']}\"\n", + " if variant_record.get(\"rearrangement_type\") else \"\")\n", + " elif feature_type == \"somatic_variant\":\n", + " feature = \"{}{}\".format(variant_record[\"gene\"] if variant_record.get(\"gene\") else \"\",\n", + " f\" {variant_record['protein_change']}\"\n", + " if variant_record.get(\"protein_change\") else \"\")\n", + " supported = True\n", + " elif feature_type == \"germline_variant\":\n", + " feature = \"{}{}\".format(variant_record[\"gene\"] if variant_record.get(\"gene\") else \"\",\n", + " f\" {variant_record['protein_change']}\"\n", + " if variant_record.get(\"protein_change\") else \"\")\n", + " supported = True\n", + " elif feature_type == \"copy_number\":\n", + " # These are all {gene} Amplification|Deletion\n", + " feature = \"{} {}\".format(variant_record[\"gene\"], variant_record[\"direction\"])\n", + " if variant_record[\"direction\"] == \"Amplification\":\n", + " supported = True\n", + " elif feature_type == \"microsatellite_stability\":\n", + " # The only one is MSI-High\n", + " feature = \"{}\".format(variant_record.get(\"status\"))\n", + " elif feature_type == \"mutational_signature\":\n", + " csn = variant_record[\"cosmic_signature_number\"]\n", + " version = variant_record[\"cosmic_signature_version\"]\n", + " feature = \"COSMIC Signature (version {}) {}\".format(version, csn)\n", + " elif feature_type == \"mutational_burden\":\n", + " clss = variant_record[\"classification\"]\n", + " min_mut = variant_record[\"minimum_mutations\"]\n", + " mut_per_mb = variant_record[\"mutations_per_mb\"]\n", + " feature = \"{}{}\".format(clss,\n", + " f\" (>= {min_mut} mutations)\" if min_mut\n", + " else (f\" (>= {mut_per_mb} mutations/Mb)\"\n", + " if mut_per_mb else \"\"))\n", + " elif feature_type == \"neoantigen_burden\":\n", + " # Doesn't seem like there are any of these\n", + " feature = \"{}\".format(variant_record[\"classification\"])\n", + " elif feature_type == \"knockdown\" or feature_type == \"silencing\":\n", + " feature = \"{}{}\".format(variant_record[\"gene\"], f\" ({variant_record['technique']})\"\n", + " if variant_record[\"technique\"] else \"\")\n", + " elif feature_type == \"aneuploidy\":\n", + " # The only one is Whole genome doubling\n", + " feature = \"{}\".format(variant_record[\"event\"])\n", + " \n", + " if not feature:\n", + " no_query_total += 1\n", + " no_query_wr.writerow([variant_id, v])\n", + " continue\n", + "\n", + " category_name = None\n", + " if any((\n", + " re.match(r\".+fs\\*\\d+$\", feature, re.IGNORECASE),\n", + " re.match(r\".+\\d+$\", feature, re.IGNORECASE)\n", + " )):\n", + " supported = False\n", + " category_name = VariantCategory.PROTEIN_CONS\n", + "\n", + " if not category_name:\n", + " category_name = moa_ft_to_variant_categories[feature_type]\n", + " \n", + " if not supported or len(feature.split()) == 1:\n", + " not_supported_feature_counts[category_name.name] += 1\n", + " not_supported_wr.writerow([variant_id, feature, feature_type, category_name])\n", + " continue\n", + "\n", + " should_be_able_to_normalize_total += 1\n", + " all_queries_wr.writerow([variant_id, feature, feature_type, category_name])\n", + "\n", + " try:\n", + " variation_norm_resp = await query_handler.normalize_handler.normalize(feature)\n", + " if not variation_norm_resp.variation_descriptor:\n", + " unable_to_normalize_wr.writerow([variant_id, feature, feature_type,\n", + " category_name, False, \"unable to normalize\", \n", + " variation_norm_resp.warnings])\n", + " unable_to_normalize_total += 1\n", + " else:\n", + " can_normalize_total += 1\n", + " vrs_id = variation_norm_resp.variation_descriptor.variation.id\n", + " able_to_normalize_wr.writerow([variant_id, feature, feature_type, \n", + " category_name, vrs_id])\n", + " except Exception as e:\n", + " unable_to_normalize_wr.writerow([variant_id, feature, feature_type, \n", + " category_name, True, str(e), None])\n", + " exception_total += 1\n", + "\n", + "# Close files\n", + "no_query_wf.close()\n", + "all_queries_wf.close()\n", + "not_supported_wf.close()\n", + "unable_to_normalize_wf.close()\n", + "able_to_normalize_wf.close()" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'Total number of variants in MOAlmanac: 423'" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"Total number of variants in MOAlmanac: {total_variants}\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Variants that we could not find queries for" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "no_query_total" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'0.00% of the total features had no queries'" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"{no_query_total / total_variants * 100:.2f}% of the total features had no queries\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Variants we do not support" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'Total number of variants we do not support in the Variation Normalizer: 244'" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "do_not_support_total_sum = sum(not_supported_feature_counts.values())\n", + "f\"Total number of variants we do not support in the Variation Normalizer: {do_not_support_total_sum}\"" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer does not support 57.68% of the total variants'" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer does not support {do_not_support_total_sum / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below are the total number of variants for each MOA Feature Type that we do not support" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'PROTEIN_CONS': 176,\n", + " 'REARRANGEMENTS': 36,\n", + " 'COPY_NUMBER': 17,\n", + " 'EXPRESSION': 11,\n", + " 'OTHER': 4,\n", + " 'EPIGENETIC_MODIFICATION': 0,\n", + " 'FUSION': 0,\n", + " 'GENE_FUNC': 0,\n", + " 'GENOTYPES_EASY': 0,\n", + " 'GENOTYPES_COMPOUND': 0,\n", + " 'REGION_DEFINED_VAR': 0,\n", + " 'INCOMPLETE_VAR': 0}" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sorted_not_sup_counts = dict(sorted(not_supported_feature_counts.items(), key=lambda x: x[1], reverse=True))\n", + "sorted_not_sup_counts" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below is the total percentage of variants for each MOA Feature Type that we do not support" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'PROTEIN_CONS': '41.61%',\n", + " 'REARRANGEMENTS': '8.51%',\n", + " 'COPY_NUMBER': '4.02%',\n", + " 'EXPRESSION': '2.60%',\n", + " 'OTHER': '0.95%',\n", + " 'EPIGENETIC_MODIFICATION': '0.00%',\n", + " 'FUSION': '0.00%',\n", + " 'GENE_FUNC': '0.00%',\n", + " 'GENOTYPES_EASY': '0.00%',\n", + " 'GENOTYPES_COMPOUND': '0.00%',\n", + " 'REGION_DEFINED_VAR': '0.00%',\n", + " 'INCOMPLETE_VAR': '0.00%'}" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "{k: f\"{v / total_variants * 100:.2f}%\" for k, v in sorted_not_sup_counts.items()}" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Variants we should be able to normalize" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "179" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "should_be_able_to_normalize_total" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer SHOULD be able to normalize 42.32% of the total variants'" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer SHOULD be able to normalize {should_be_able_to_normalize_total / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Variants we were not able to normalize\n", + "\n", + "Either due to a bug or an unsupported query type in Variation Normalizer" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "unable_to_normalize_total" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer was unable to normalize 0.0% of the total variants'" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer was unable to normalize {unable_to_normalize_total / total_variants * 100}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Breakdown of the variants we weren't able to normalize\n", + "\n", + "In this section, we breakdown the reasons on why we weren't able to normalize variants." + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [], + "source": [ + "unable_to_tokenize = 0\n", + "unable_to_find_valid = 0\n", + "other = 0\n", + "with open(\"unable_to_normalize_queries.csv\", \"r\") as f:\n", + " reader = csv.reader(f, delimiter=\"\\t\")\n", + " next(reader)\n", + " for row in reader:\n", + " if \"Unable to find valid result\" in row[-1]:\n", + " unable_to_find_valid += 1\n", + " elif \"Unable to tokenize\" in row[-1]:\n", + " unable_to_tokenize += 1\n", + " else:\n", + " other += 1" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Due to not passing validation checks\n", + "\n", + "The Variation Normalizer performs validation checks on the input query (such as reference sequence). If these validation checks fail, then the input query will fail to normalize." + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer found 0 invalid variants (This is 0.00% of the total variants).'" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer found {unable_to_find_valid} invalid variants (This is {unable_to_find_valid / total_variants * 100:.2f}% of the total variants).\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Due to tokenization \n", + "\n", + "The Variation Normalizer will tokenize the input query to determine the kind of token. It is limited in the kinds of tokens it accepts, so these tokens are not yet supported in the Variation Normalizer. " + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer was unable to tokenize 0 variants (0.00% of the total variants).'" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer was unable to tokenize {unable_to_tokenize} variants ({unable_to_tokenize / total_variants * 100:.2f}% of the total variants).\"" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer was unable to normalize 0 variants due to other issues (This is 0.00% of the total variants).'" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer was unable to normalize {other} variants due to other issues (This is {other / total_variants * 100:.2f}% of the total variants).\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Variant queries that raised an exception during normalization" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer raised an exception for 0.00% of the total variants'" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer raised an exception for {exception_total / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Variants we were able to normalize" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "179" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "can_normalize_total" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer successfully normalized 100.00% of the variants we SHOULD be able to normalize'" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer successfully normalized {can_normalize_total / should_be_able_to_normalize_total * 100:.2f}% of the variants we SHOULD be able to normalize\"" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'The Variation Normalizer successfully normalized 42.32% of the total variants'" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f\"The Variation Normalizer successfully normalized {can_normalize_total / total_variants * 100:.2f}% of the total variants\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "variation-normalization-KPVKcmjd", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.3" + }, + "orig_nbformat": 4, + "vscode": { + "interpreter": { + "hash": "0be8ba9a7b89517724a412b9d40e184059795303560bd1108143a8aed13113be" + } + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/analysis/moa/no_query.csv b/analysis/moa/no_query.csv new file mode 100644 index 0000000..b808f18 --- /dev/null +++ b/analysis/moa/no_query.csv @@ -0,0 +1 @@ +variant_id feature diff --git a/analysis/moa/not_supported_variants.csv b/analysis/moa/not_supported_variants.csv new file mode 100644 index 0000000..aaf471b --- /dev/null +++ b/analysis/moa/not_supported_variants.csv @@ -0,0 +1,245 @@ +variant_id query moa_feature_type category +1 BCR--ABL1 Fusion rearrangement Rearrangements +12 ALK Fusion rearrangement Rearrangements +15 ALK rearrangement Rearrangements +18 ALK Translocation rearrangement Rearrangements +21 BRD4 t(15;19) Translocation rearrangement Rearrangements +22 CCND1 t(11;14) Translocation rearrangement Rearrangements +24 CCND3 t(6;14) Translocation rearrangement Rearrangements +25 COL1A1--PDGFB Fusion rearrangement Rearrangements +26 EML4--ALK Fusion rearrangement Rearrangements +28 ESRP1--RAF1 Fusion rearrangement Rearrangements +30 EWSR1--FLI1 Fusion rearrangement Rearrangements +31 FGFR2--TACC3 Fusion rearrangement Rearrangements +32 FGFR2 Fusion rearrangement Rearrangements +34 FGFR2 rearrangement Protein Consequence +36 FGFR3 Fusion rearrangement Rearrangements +37 FGFR3--NSD2 Fusion rearrangement Rearrangements +38 IGH t(11;14)(q13;q32) Translocation rearrangement Rearrangements +39 IGH t(4;14)(q16;q32) Translocation rearrangement Rearrangements +40 NTRK1 Translocation rearrangement Rearrangements +42 NTRK2 Fusion rearrangement Rearrangements +43 NTRK2 Translocation rearrangement Rearrangements +46 NTRK3 Translocation rearrangement Rearrangements +48 NTRK3 Fusion rearrangement Rearrangements +49 PDGFRA rearrangement Rearrangements +50 FIP1L1--PDGFRA Fusion rearrangement Rearrangements +51 BCR--PDGFRA Fusion rearrangement Rearrangements +52 PDGFRB rearrangement Rearrangements +53 PDGFRB 5q31-33 Translocation rearrangement Rearrangements +54 PDGFRB 4p12 Translocation rearrangement Rearrangements +55 RET rearrangement Rearrangements +57 RET Fusion rearrangement Rearrangements +62 ROS1 Fusion rearrangement Rearrangements +64 RUNX1--RUNX1T1 Fusion rearrangement Rearrangements +65 SLC45A3--BRAF Fusion rearrangement Rearrangements +67 TMPRSS2--ERG Fusion rearrangement Rearrangements +72 ABL1 somatic_variant Protein Consequence +79 ABL1 somatic_variant Protein Consequence +111 AKT1 somatic_variant Protein Consequence +113 AKT2 somatic_variant Protein Consequence +114 AKT3 somatic_variant Protein Consequence +123 ARID1A somatic_variant Protein Consequence +124 ARID1A somatic_variant Protein Consequence +125 ARID1A somatic_variant Protein Consequence +126 ASXL1 somatic_variant Protein Consequence +127 ASXL1 somatic_variant Protein Consequence +128 ATM somatic_variant Protein Consequence +129 ATM somatic_variant Protein Consequence +130 ATM somatic_variant Protein Consequence +135 ATM somatic_variant Protein Consequence +136 BARD1 somatic_variant Protein Consequence +143 BCOR somatic_variant Protein Consequence +144 BCOR somatic_variant Protein Consequence +145 BCOR somatic_variant Protein Consequence +147 BCR somatic_variant Protein Consequence +148 BLM somatic_variant Protein Consequence +172 BRAF somatic_variant Protein Consequence +193 BRCA1 somatic_variant Protein Consequence +196 BRCA1 somatic_variant Protein Consequence +209 BRCA2 somatic_variant Protein Consequence +215 BRCA2 somatic_variant Protein Consequence +222 BRCA2 somatic_variant Protein Consequence +227 BRIP1 somatic_variant Protein Consequence +234 CDK12 somatic_variant Protein Consequence +235 CHEK1 somatic_variant Protein Consequence +242 CHEK2 somatic_variant Protein Consequence +249 CTNNB1 somatic_variant Protein Consequence +251 DNMT3A somatic_variant Protein Consequence +252 DNMT3A somatic_variant Protein Consequence +253 DNMT3A somatic_variant Protein Consequence +255 EGFR somatic_variant Protein Consequence +260 EGFR somatic_variant Protein Consequence +280 EGFR somatic_variant Protein Consequence +283 EGFR somatic_variant Protein Consequence +285 EGFR somatic_variant Protein Consequence +289 ERBB2 somatic_variant Protein Consequence +290 ERBB2 somatic_variant Protein Consequence +291 ERBB3 somatic_variant Protein Consequence +292 ERCC2 somatic_variant Protein Consequence +295 ESR1 somatic_variant Protein Consequence +296 ETV6 somatic_variant Protein Consequence +297 ETV6 somatic_variant Protein Consequence +298 EZH2 somatic_variant Protein Consequence +299 EZH2 somatic_variant Protein Consequence +305 FANCL somatic_variant Protein Consequence +306 FBXW7 somatic_variant Protein Consequence +311 FLCN somatic_variant Protein Consequence +314 FLCN somatic_variant Protein Consequence +320 IDH1 somatic_variant Protein Consequence +332 IDH2 somatic_variant Protein Consequence +337 JAK1 somatic_variant Protein Consequence +340 JAK2 somatic_variant Protein Consequence +348 KIT somatic_variant Protein Consequence +349 KIT somatic_variant Protein Consequence +359 KIT somatic_variant Protein Consequence +360 KIT somatic_variant Protein Consequence +368 KIT somatic_variant Protein Consequence +372 KIT somatic_variant Protein Consequence +378 KRAS somatic_variant Protein Consequence +380 KRAS somatic_variant Protein Consequence +382 KRAS somatic_variant Protein Consequence +384 KRAS somatic_variant Protein Consequence +391 KRAS p.G12 somatic_variant Protein Consequence +392 KRAS p.G13 somatic_variant Protein Consequence +393 KRAS p.Q61 somatic_variant Protein Consequence +412 MC1R somatic_variant Protein Consequence +414 MET somatic_variant Protein Consequence +415 MET somatic_variant Protein Consequence +416 MET somatic_variant Protein Consequence +420 MLH3 somatic_variant Protein Consequence +422 MSH2 somatic_variant Protein Consequence +423 MSH6 somatic_variant Protein Consequence +424 MTOR somatic_variant Protein Consequence +425 MYH somatic_variant Protein Consequence +426 NFE2L2 somatic_variant Protein Consequence +427 NRAS somatic_variant Protein Consequence +429 NRAS somatic_variant Protein Consequence +449 PALB2 somatic_variant Protein Consequence +457 PBRM1 somatic_variant Protein Consequence +458 PDGFRA somatic_variant Protein Consequence +461 PDGFRA somatic_variant Protein Consequence +463 PBRM1 somatic_variant Protein Consequence +464 PIK3CA somatic_variant Protein Consequence +465 PIK3CA somatic_variant Protein Consequence +487 PIK3CB somatic_variant Protein Consequence +492 POLD1 somatic_variant Protein Consequence +496 POLE somatic_variant Protein Consequence +499 PRPF8 somatic_variant Protein Consequence +500 PTEN somatic_variant Protein Consequence +501 PTEN somatic_variant Protein Consequence +502 PTEN somatic_variant Protein Consequence +506 PTEN somatic_variant Protein Consequence +511 PTPN11 somatic_variant Protein Consequence +512 RAD51B somatic_variant Protein Consequence +513 RAD51C somatic_variant Protein Consequence +520 RAD51D somatic_variant Protein Consequence +527 RAD54L somatic_variant Protein Consequence +528 RBM10 somatic_variant Protein Consequence +531 RET somatic_variant Protein Consequence +533 RUNX1 somatic_variant Protein Consequence +534 RUNX1 somatic_variant Protein Consequence +537 SETBP1 somatic_variant Protein Consequence +542 SETBP1 somatic_variant Protein Consequence +557 SF3B1 somatic_variant Protein Consequence +562 SMARCA4 somatic_variant Protein Consequence +563 SMARCA4 somatic_variant Protein Consequence +564 SMARCA4 somatic_variant Protein Consequence +565 SPOP somatic_variant Protein Consequence +568 STAG2 somatic_variant Protein Consequence +569 STAG2 somatic_variant Protein Consequence +570 STAG2 somatic_variant Protein Consequence +571 TET2 somatic_variant Protein Consequence +572 TP53 somatic_variant Protein Consequence +573 TP53 somatic_variant Protein Consequence +574 TP53 somatic_variant Protein Consequence +575 TP53 somatic_variant Protein Consequence +576 TP53 somatic_variant Protein Consequence +580 TSC1 somatic_variant Protein Consequence +581 TSC1 somatic_variant Protein Consequence +582 TSC1 somatic_variant Protein Consequence +585 TSC1 somatic_variant Protein Consequence +586 TSC2 somatic_variant Protein Consequence +587 TSC2 somatic_variant Protein Consequence +588 TSC2 somatic_variant Protein Consequence +589 TSC2 somatic_variant Protein Consequence +592 ZRSR2 somatic_variant Protein Consequence +593 ZRSR2 somatic_variant Protein Consequence +594 ATM germline_variant Protein Consequence +595 ATM germline_variant Protein Consequence +596 ATM germline_variant Protein Consequence +597 BARD1 germline_variant Protein Consequence +603 BRCA1 germline_variant Protein Consequence +612 BRCA1 germline_variant Protein Consequence +622 BRCA2 germline_variant Protein Consequence +634 BRCA2 germline_variant Protein Consequence +640 CHEK1 germline_variant Protein Consequence +646 CHEK2 germline_variant Protein Consequence +652 CHEK2 germline_variant Protein Consequence +653 EPCAM germline_variant Protein Consequence +656 LIMK2 p.G574Rfs*12 germline_variant Protein Consequence +657 LIMK2 p.C582Lfs*4 germline_variant Protein Consequence +658 LIMK2 p.G684Tfs*16 germline_variant Protein Consequence +659 MLH1 germline_variant Protein Consequence +660 MLH3 germline_variant Protein Consequence +662 MRE11 p.H356Tfs*34 germline_variant Protein Consequence +663 MRE11 p.L7fs*18 germline_variant Protein Consequence +664 MSH2 germline_variant Protein Consequence +666 MSH6 germline_variant Protein Consequence +668 NF1 germline_variant Protein Consequence +669 PALB2 germline_variant Protein Consequence +676 PALB2 germline_variant Protein Consequence +677 PMS2 germline_variant Protein Consequence +678 POLE2 p.L469Ffs*17 germline_variant Protein Consequence +679 POT1 p.D617Efs*9 germline_variant Protein Consequence +681 POT1 p.N75Kfs*16 germline_variant Protein Consequence +682 RAD51C germline_variant Protein Consequence +688 RAD51D germline_variant Protein Consequence +694 RB1 germline_variant Protein Consequence +695 TP53 germline_variant Protein Consequence +700 ARID1A Deletion copy_number Copy Number +706 BRCA2 Deletion copy_number Copy Number +720 CDKN2A Deletion copy_number Copy Number +722 CDKN2C Deletion copy_number Copy Number +723 CDKN2C Deletion copy_number Copy Number +745 FBXW7 Deletion copy_number Copy Number +755 KEAP1 Deletion copy_number Copy Number +763 MIR17HG Deletion copy_number Copy Number +769 PBRM1 Deletion copy_number Copy Number +771 PTEN Deletion copy_number Copy Number +778 RB1 Deletion copy_number Copy Number +779 TP53 Deletion copy_number Copy Number +781 MSI-High microsatellite_stability Rearrangements +786 COSMIC Signature (version 2) 10 mutational_signature Protein Consequence +789 COSMIC Signature (version 2) 2 mutational_signature Protein Consequence +791 COSMIC Signature (version 2) 3 mutational_signature Protein Consequence +797 COSMIC Signature (version 2) 4 mutational_signature Protein Consequence +799 COSMIC Signature (version 2) 5 mutational_signature Protein Consequence +803 High mutational_burden Other +805 High (>= 178 mutations) mutational_burden Other +806 High (>= 100 mutations) mutational_burden Other +808 High (>= 10 mutations/Mb) mutational_burden Other +809 ATM (shRNA) knockdown Expression +810 B2M (CRISPR-Cas9) knockdown Expression +811 CDK12 (shRNA) knockdown Expression +812 CDK12 (siRNA) knockdown Expression +813 CPT1A (shRNA) knockdown Expression +814 RAD17 (shRNA) knockdown Expression +816 RAD50 (shRNA) knockdown Expression +817 TAP2 (CRISPR-Cas9) knockdown Expression +818 PPARGC1A (CRSPR-Cas9) knockdown Expression +819 Whole genome doubling aneuploidy Copy Number +833 RB1 (shRNA) knockdown Expression +834 USP11 (siRNA) knockdown Expression +835 ALK--EML4 Fusion rearrangement Rearrangements +836 BRCA1 somatic_variant Protein Consequence +837 BRCA1 somatic_variant Protein Consequence +841 BRCA2 somatic_variant Protein Consequence +846 RB1 somatic_variant Protein Consequence +847 RB1 somatic_variant Protein Consequence +848 ATRX Deletion copy_number Copy Number +849 BRCA1 Deletion copy_number Copy Number +853 CDKN2C Deletion copy_number Copy Number +862 RB1 Deletion copy_number Copy Number +863 FGFR1 rearrangement Protein Consequence +873 ESR1 somatic_variant Protein Consequence diff --git a/analysis/moa/should_be_able_to_normalize_queries.csv b/analysis/moa/should_be_able_to_normalize_queries.csv new file mode 100644 index 0000000..b09f525 --- /dev/null +++ b/analysis/moa/should_be_able_to_normalize_queries.csv @@ -0,0 +1,180 @@ +variant_id query moa_feature_type category +71 ABL1 p.T315I somatic_variant Protein Consequence +73 ABL1 p.T315A somatic_variant Protein Consequence +75 ABL1 p.F317L somatic_variant Protein Consequence +76 ABL1 p.F317V somatic_variant Protein Consequence +77 ABL1 p.F317I somatic_variant Protein Consequence +78 ABL1 p.F317C somatic_variant Protein Consequence +80 ABL1 p.E255K somatic_variant Protein Consequence +81 ABL1 p.E255V somatic_variant Protein Consequence +82 ABL1 p.Y253H somatic_variant Protein Consequence +83 ABL1 p.F359V somatic_variant Protein Consequence +84 ABL1 p.F359C somatic_variant Protein Consequence +85 ABL1 p.F359I somatic_variant Protein Consequence +97 ABL1 p.V299L somatic_variant Protein Consequence +108 ABL1 p.T315I somatic_variant Protein Consequence +112 AKT1 p.E17K somatic_variant Protein Consequence +115 ALK p.G1202R somatic_variant Protein Consequence +116 ALK p.F1174C somatic_variant Protein Consequence +117 ALK p.L1196M somatic_variant Protein Consequence +118 ALK p.G1269A somatic_variant Protein Consequence +119 ALK p.S1206Y somatic_variant Protein Consequence +120 AR p.T878A somatic_variant Protein Consequence +121 AR p.L702H somatic_variant Protein Consequence +122 ARAF p.S214C somatic_variant Protein Consequence +134 ATM p.A1127D somatic_variant Protein Consequence +146 BCOR p.N1425S somatic_variant Protein Consequence +149 BRAF p.V600E somatic_variant Protein Consequence +151 BRAF p.V600K somatic_variant Protein Consequence +250 DNMT3A p.R882H somatic_variant Protein Consequence +254 EGFR p.T790M somatic_variant Protein Consequence +267 EGFR p.L858R somatic_variant Protein Consequence +284 EGFR p.L858R somatic_variant Protein Consequence +286 EGFR p.L858R somatic_variant Protein Consequence +294 ERRFI1 p.E384* somatic_variant Protein Consequence +300 EZH2 p.Y646* somatic_variant Protein Consequence +301 EZH2 p.Y646F somatic_variant Protein Consequence +302 EZH2 p.Y646N somatic_variant Protein Consequence +303 EZH2 p.A682G somatic_variant Protein Consequence +304 EZH2 p.A692V somatic_variant Protein Consequence +307 FGFR3 p.R248C somatic_variant Protein Consequence +308 FGFR3 p.S249C somatic_variant Protein Consequence +309 FGFR3 p.G370C somatic_variant Protein Consequence +310 FGFR3 p.Y373C somatic_variant Protein Consequence +317 FLT3 p.F691L somatic_variant Protein Consequence +318 FLT3 p.K663Q somatic_variant Protein Consequence +319 GATA3 p.M294K somatic_variant Protein Consequence +323 IDH1 p.R132H somatic_variant Protein Consequence +324 IDH1 p.R132C somatic_variant Protein Consequence +329 IDH2 p.R140Q somatic_variant Protein Consequence +330 IDH2 p.R172S somatic_variant Protein Consequence +331 IDH2 p.R172K somatic_variant Protein Consequence +334 IDH2 p.R140Q somatic_variant Protein Consequence +338 JAK1 p.V656F somatic_variant Protein Consequence +339 JAK1 p.A634D somatic_variant Protein Consequence +341 JAK2 p.V617F somatic_variant Protein Consequence +342 JAK3 p.A572T somatic_variant Protein Consequence +343 JAK3 p.M511I somatic_variant Protein Consequence +344 JAK3 p.L857Q somatic_variant Protein Consequence +352 KIT p.T670I somatic_variant Protein Consequence +353 KIT p.V654A somatic_variant Protein Consequence +361 KIT p.W557C somatic_variant Protein Consequence +362 KIT p.W557G somatic_variant Protein Consequence +363 KIT p.W557R somatic_variant Protein Consequence +364 KIT p.V559A somatic_variant Protein Consequence +365 KIT p.V559G somatic_variant Protein Consequence +366 KIT p.L576P somatic_variant Protein Consequence +367 KIT p.K642E somatic_variant Protein Consequence +369 KIT p.D816H somatic_variant Protein Consequence +374 KIT p.D816V somatic_variant Protein Consequence +387 KRAS p.G12C somatic_variant Protein Consequence +390 KRAS p.G12D somatic_variant Protein Consequence +402 MAP2K1 p.P124L somatic_variant Protein Consequence +403 MAP2K1 p.Q56P somatic_variant Protein Consequence +408 MAP2K1 p.C121S somatic_variant Protein Consequence +410 MAP2K2 p.Q60P somatic_variant Protein Consequence +411 MAPK1 p.E322K somatic_variant Protein Consequence +413 MET p.T1010I somatic_variant Protein Consequence +421 MPL p.W515L somatic_variant Protein Consequence +432 NRAS p.G12A somatic_variant Protein Consequence +433 NRAS p.G12C somatic_variant Protein Consequence +434 NRAS p.G12D somatic_variant Protein Consequence +435 NRAS p.G12R somatic_variant Protein Consequence +436 NRAS p.G12S somatic_variant Protein Consequence +437 NRAS p.G12V somatic_variant Protein Consequence +438 NRAS p.G13A somatic_variant Protein Consequence +439 NRAS p.G13D somatic_variant Protein Consequence +440 NRAS p.G13R somatic_variant Protein Consequence +441 NRAS p.G13V somatic_variant Protein Consequence +442 NRAS p.Q61E somatic_variant Protein Consequence +443 NRAS p.Q61H somatic_variant Protein Consequence +444 NRAS p.Q61L somatic_variant Protein Consequence +446 NRAS p.Q61P somatic_variant Protein Consequence +447 NRAS p.Q61R somatic_variant Protein Consequence +459 PDGFRA p.D842V somatic_variant Protein Consequence +467 PIK3CA p.E545Q somatic_variant Protein Consequence +468 PIK3CA p.C420R somatic_variant Protein Consequence +469 PIK3CA p.E542K somatic_variant Protein Consequence +470 PIK3CA p.E542Q somatic_variant Protein Consequence +471 PIK3CA p.E545A somatic_variant Protein Consequence +472 PIK3CA p.E545D somatic_variant Protein Consequence +474 PIK3CA p.E545G somatic_variant Protein Consequence +475 PIK3CA p.E545K somatic_variant Protein Consequence +476 PIK3CA p.G1049R somatic_variant Protein Consequence +477 PIK3CA p.G1049S somatic_variant Protein Consequence +478 PIK3CA p.H1047L somatic_variant Protein Consequence +479 PIK3CA p.H1047R somatic_variant Protein Consequence +480 PIK3CA p.H1047Y somatic_variant Protein Consequence +481 PIK3CA p.H701P somatic_variant Protein Consequence +482 PIK3CA p.M1043I somatic_variant Protein Consequence +484 PIK3CA p.P539R somatic_variant Protein Consequence +485 PIK3CA p.Q546K somatic_variant Protein Consequence +486 PIK3CA p.Y1021C somatic_variant Protein Consequence +488 POLD1 p.D316H somatic_variant Protein Consequence +489 POLD1 p.D316G somatic_variant Protein Consequence +490 POLD1 p.R409W somatic_variant Protein Consequence +491 POLD1 p.L474P somatic_variant Protein Consequence +495 POLE p.L424V somatic_variant Protein Consequence +529 RET p.V804M somatic_variant Protein Consequence +530 RET p.M918T somatic_variant Protein Consequence +535 SETBP1 p.E858K somatic_variant Protein Consequence +536 SETBP1 p.T864M somatic_variant Protein Consequence +538 SETBP1 p.D868N somatic_variant Protein Consequence +539 SETBP1 p.D868Y somatic_variant Protein Consequence +540 SETBP1 p.S869C somatic_variant Protein Consequence +541 SETBP1 p.G870S somatic_variant Protein Consequence +543 SF3B1 p.E622Q somatic_variant Protein Consequence +544 SF3B1 p.E622D somatic_variant Protein Consequence +545 SF3B1 p.Y623C somatic_variant Protein Consequence +546 SF3B1 p.R625C somatic_variant Protein Consequence +547 SF3B1 p.R625H somatic_variant Protein Consequence +548 SF3B1 p.N626H somatic_variant Protein Consequence +549 SF3B1 p.N626Y somatic_variant Protein Consequence +550 SF3B1 p.N626D somatic_variant Protein Consequence +551 SF3B1 p.H662R somatic_variant Protein Consequence +552 SF3B1 p.T663P somatic_variant Protein Consequence +553 SF3B1 p.K666N somatic_variant Protein Consequence +554 SF3B1 p.K666T somatic_variant Protein Consequence +555 SF3B1 p.K666E somatic_variant Protein Consequence +556 SF3B1 p.K700E somatic_variant Protein Consequence +558 SF3B1 p.G740E somatic_variant Protein Consequence +559 SF3B1 p.G740V somatic_variant Protein Consequence +560 SF3B1 p.G742D somatic_variant Protein Consequence +561 SF3B1 p.D781E somatic_variant Protein Consequence +654 IL12RB1 p.Q32* germline_variant Protein Consequence +655 IL12RB1 p.Q542* germline_variant Protein Consequence +661 MRE11 p.R576* germline_variant Protein Consequence +680 POT1 p.R363* germline_variant Protein Consequence +696 AR Amplification copy_number Copy Number +701 AURKA Amplification copy_number Copy Number +703 AURKB Amplification copy_number Copy Number +704 BRAF Amplification copy_number Copy Number +707 CCND1 Amplification copy_number Copy Number +708 CCND1 Amplification copy_number Copy Number +709 CCNE1 Amplification copy_number Copy Number +710 CD274 Amplification copy_number Copy Number +716 CDK4 Amplification copy_number Copy Number +724 CRKL Amplification copy_number Copy Number +725 EGFR Amplification copy_number Copy Number +726 ERBB2 Amplification copy_number Copy Number +744 ESR1 Amplification copy_number Copy Number +746 FGFR1 Amplification copy_number Copy Number +750 FGFR2 Amplification copy_number Copy Number +754 HIF1a Amplification copy_number Copy Number +756 KIT Amplification copy_number Copy Number +757 MDM2 Amplification copy_number Copy Number +758 MET Amplification copy_number Copy Number +762 MIR17HG Amplification copy_number Copy Number +764 MRE11 Amplification copy_number Copy Number +765 MYC Amplification copy_number Copy Number +766 MYC Amplification copy_number Copy Number +767 PAK1 Amplification copy_number Copy Number +770 PIK3CA Amplification copy_number Copy Number +780 TPX2 Amplification copy_number Copy Number +854 MAP2K4 Amplification copy_number Copy Number +857 MAPK7 Amplification copy_number Copy Number +858 MYOCD Amplification copy_number Copy Number +859 PDGFRA Amplification copy_number Copy Number +868 IDH1 p.R132G somatic_variant Protein Consequence +869 IDH1 p.R132S somatic_variant Protein Consequence +870 IDH1 p.R132L somatic_variant Protein Consequence diff --git a/analysis/moa/unable_to_normalize_queries.csv b/analysis/moa/unable_to_normalize_queries.csv new file mode 100644 index 0000000..cc0f40c --- /dev/null +++ b/analysis/moa/unable_to_normalize_queries.csv @@ -0,0 +1 @@ +variant_id query moa_feature_type category exception_raised message warnings diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..fdfcfad --- /dev/null +++ b/requirements.txt @@ -0,0 +1,9 @@ +variation-normalizer == 0.5.5 +civicpy ~= 3.0.0 +python-dotenv +ipykernel +jupyter +plotly +pandas +nbformat +requests