Open larrybabb opened 6 months ago
I think we should be checking reference alleles on all format types spdi
, gnomad
, beacon
and hgvs
.
@larrybabb I think this is related to #151 . Once added, I can update the normalizer's vrs-python endpoints (which haven't been updated in a long time) to accept kwargs
In clinvar there's a variant NM_006087.3:c.900C>A (267781) that has no hgvs or spdi or location data. When I used the metakb variant normalizer service translate_from which uses the vrs-python translate from it returned a valid VRS object.
So, tried to lookup this variant in the clingen allele registry and found that it failed for the following reason
I did not investigate further to see if vrs-python ignores checking the Reference Alleles or not, because I assume it to be true.
I don't think vrs-python translate_from should accept hgvs expressions that contain referenceAlleles that do not actually match the nucleotides specified by the hgvs expression. Like the Clingen Allele Registry, we should probably throw an exception.