diff --git a/service/src/main/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java b/service/src/main/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java index d672a3cd..52f8252d 100644 --- a/service/src/main/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java +++ b/service/src/main/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java @@ -114,7 +114,7 @@ public VariantAnnotationSummary getAnnotationSummaryForCanonical(VariantAnnotati if (annotationSummary != null) { if (canonicalTranscript == null && annotation.getIntergenicConsequences() != null && !annotation.getIntergenicConsequences().isEmpty()) { - // Set variantClassification to "IGR" and when variant is "intergenic_variant". + // Set intergenicConsequenceSummaries when variant is "intergenic_variant", add variant classification based on consequence terms. // This is useful for genome nexus annotation pipeline, so when doing curation, those mutations will be filtered out by "IGR" rule, instead of being imported as "MUTATED". List intergenicConsequenceSummaries = new ArrayList<>(); for (IntergenicConsequences intergenicConsequence : annotation.getIntergenicConsequences()) {