![]() ![]() I think you are talking about two different ClinVar annotations. When the variants are normalized, VEP matches the ref and alt alleles with the ones from the ClinVar VCF file as described above (using custom annotation). #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FL202109121Ĭhr4 55141030. Here is example of a special example, vep missed both clin_sig, but annovar get the right clin_sig of origin oneĬhr4ĕ5141030ĕ5141030 - GAGGGAĒ8586 Gastrointestinal_stromal_tumor Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890 no_assertion_criteria_provided Pathogenic
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