I've got annotations for splicing variants in a format like this (this is one variant):

  • Variant: NM_004092.3:c.88+5G>A
  • Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23)

I want to extract which acceptor/donor sites are lost or gained (in this case lost causing intron retention). In other words, the genomic location of the sequence that is retained in mRNA.

I parsed the variant HGVS ID using ensembl VEP (like this) without problems, giving me the genomic location of this variant. However, VEP seems to not like "r." annotations for the effect: I tried ensembl VEP again with RNA, protein, and both annotations, none of which worked.

Is there a tool that can parse these annotations for me? I've got too many to do it by hand.

Note on RNA splicing

RNA splicing and acceptor and donor sites:

An introns contains: a 5' donor site, a branch site located near the 3' site and a 3' acceptor site. Both the donor and acceptor are required for splicing along with the branch site.



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