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service/src/main/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationSummaryServiceImpl.java

@@ -113,11 +113,12 @@ public VariantAnnotationSummary getAnnotationSummaryForCanonical(VariantAnnotati
 
         if (annotationSummary != null) {
             if (canonicalTranscript == null && annotation.getIntergenicConsequences() != null && !annotation.getIntergenicConsequences().isEmpty()) {
-                // Set variantClassification and consequence to "IGR" and "intergenic_variant" when variant is "intergenic_variant".
+                // Set variantClassification to "IGR" and when variant is "intergenic_variant".
                 // 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".
                 IntergenicConsequenceSummary intergenicConsequenceSummary = new IntergenicConsequenceSummary();
-                // get related fields from annotation.getIntergenicConsequences() and add one more field "variantClassification" from variantClassificationResolver
+                // Get related fields from annotation.getIntergenicConsequences() and add "variantClassification"
                 intergenicConsequenceSummary.setVariantClassification(this.variantClassificationResolver.resolve(annotation, canonicalTranscript));
+                // Use the first intergenic consequence to set impact, variantAllele and consequenceTerms
                 intergenicConsequenceSummary.setImpact(annotation.getIntergenicConsequences().get(0).getImpact());
                 intergenicConsequenceSummary.setVariantAllele(annotation.getIntergenicConsequences().get(0).getVariantAllele());
                 intergenicConsequenceSummary.setConsequenceTerms(annotation.getIntergenicConsequences().get(0).getConsequenceTerms());