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Description
PathogenicityProposition and OncogenicityProposition both support a geneContextQualifier
, which is described as "a gene impacted by the variant, which may contribute to the association described in the Proposition."
In many cases, there are multiple transcripts for a single gene, and a variant may have different impacts on different transcripts. When making a pathogenicity or oncogenicity assertion, pathologists and variant scientists must sometimes determine which transcripts are likely to be biologically relevant (e.g., depending on tissue type and expression data). It would be useful to be able to capture this determination discretely in VA-spec.
Since gene is already a qualifier, a transcript qualifier seemed intuitive to me, but it could also be an evidence line.