Variant notation quick reference
Recall the difference between VCF representation, HGVS variant description, and gene nomenclature.
VCF What do REF and ALT mean in a VCF row? They are alleles relative to the reference genome. REF is the reference allele at the VCF position; ALT is the alternate allele observed or called. The meaning depends on the reference assembly and normalized representation. HGVS trap Can I write the variant as just BRCA1 5382insC? A legacy note gives a gene and old-style variant shorthand. Your response Use an HGVS expression tied to a reference sequence, such as a transcript accession, and keep the gene symbol in a separate field. Mixing gene name, legacy shorthand, and variant description…
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