Skip to content

Clinvar link (and annotations) on Variant Details is for a different allele (multiple alleles for a dbSNP for different amino acid changes) #1131

Description

@tonydisera

Image

Image

while the ClinVar Link from dbSNP shows the options Arg= (which is usually a silent Missense) and Gln>Arg.

Ah. Now I think I can isolate this bug. Thank you for all of the details! So rs1605 is interesting because it has multiple alleles. And I suspect that gene.iobio is creating the ClinVar link based on matching to the dbSNP id. I know exactly where to look in the gene.iobio code now.
Image

I incorrectly assumed that a dbSNP entry (rs…) with multiple alleles only happen when the alleles result in the same amino acid (due to degenerate genetic code, different codons translating into the same amino acid). But I just learned that there are other multiple allele scenarios that can result in different amino acids, like in rs6025 where different alleles result in different HGVS protein annotations. Another interesting wrinkle is that dbSNP rs6025 show C/A/T alleles, which might explain why gene.iobio is incorrectly linking to the Arg= result.
Image
Image
So I will dig into the different scenarios and account for this in gene.iobio.

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

Labels

No labels
No labels

Type

No type

Projects

No projects

    Milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions