Merge pull request #1703 from alliance-genome/SCRUM-4442_handle_x_ami…

…no_acids SCRUM-4442 (update) Handle ambiguous codon change
alliance-genome · Nov 6, 2024 · af86c3f · af86c3f
2 parents 7d9b6b9 + 8de39ca
commit af86c3f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/...alliancegenome/curation_api/services/validation/dto/fms/VepTranscriptFmsDTOValidator.java b/...alliancegenome/curation_api/services/validation/dto/fms/VepTranscriptFmsDTOValidator.java
@@ -168,7 +168,7 @@ public PredictedVariantConsequence validateTranscriptLevelConsequence(VepTxtDTO
 		String variantAminoAcids = null;
 		if (StringUtils.isNotBlank(dto.getAminoAcids())) {
 			String[] refVarAminoAcids = dto.getAminoAcids().split("/");
-			if (refVarAminoAcids.length == 1 && dto.getConsequence().contains("synonymous_variant")) {
+			if (refVarAminoAcids.length == 1 && (Objects.equals(dto.getAminoAcids(), "X") || dto.getConsequence().contains("synonymous_variant"))) {
 				referenceAminoAcids = refVarAminoAcids[0];
 				variantAminoAcids = refVarAminoAcids[0];
 			} else if (refVarAminoAcids.length == 2) {