Support transcript variants with specification of underlying genomic reference

[reece]

In https://groups.google.com/g/hgvs-discuss/c/7I1jP5m7bvk/m/wjUzIk0zAwAJ, Matt Ducar wrote:

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I get the following printout:
NC_000017.10:g.7578369A>C

NM_000546.5:c.559+2T>G

That isn't the output I expected based on the HGVS documentation at:
https://varnomen.hgvs.org/bg-material/numbering/

Which states: "a coding DNA reference sequence does not contain intron or 5’ and 3’ gene flanking sequences and can therefore not be used as a reference to describe variants in these regions see Reference Sequences."

The expected annotation would instead be:
NC_000017.10(NM_000546.5):c.559+2T>G

Neither parsing nor generating this syntax is currently supported by hgvs. (This part of the guidelines was added long after the parser and data model were in place.)

The goal of this issue is to implement full support, i.e.:

• parsing variants like "NC_000017.10(NM_000546.5):c.559+2T>G" so that the genomic access is stored (probably in the SequenceVariant)
• When a genomic variant is projected to a transcript, the genomic accession is added to the resulting transcript record
• When a transcript variant is stringified, the genomic reference is included if present
• Consider a config option to require that intronic variants specify a genomic reference. i.e., strictly reject parsing or generating variants like "NM_000546.5:c.559+2T>G"

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