lib: fix HGVS annotator #TASK-310
@@ -555,6 +555,10 @@ public class HgvsProteinCalculator {
}
} else {
cdsVariantStartPosition = HgvsCalculator.getCdsStart(transcript, variant.getStart());
+ // A deletion happens in the first 2 nucleotides of an incomplete transcript
+ if (cdsVariantStartPosition < 3 && transcriptUtils.hasUnconfirmedStart()) {
+ return null;
+ }
}
} else {
if (variant.getStart() <= transcript.getGenomicCodingEnd() && variant.getEnd() > transcript.getGenomicCodingEnd()) {
