[ensembl-dev] Error msg in VEP using HGVS option

Sarah Hunt seh at ebi.ac.uk
Wed Nov 13 15:02:42 GMT 2013


Hi Duarte,

Thanks for this really useful example - we will add it to our tests.

I notice that the insertion allele is being called
ENSP00000364163.3:p.Leu16_Cys17insLeu which is an accurate description
of the change, but not the HGVS recommended
ENSP00000364163.3:p.Leu16dup. (The reason for this is that only the
sequence prior to the reference allele was being checked for possible
duplications, but for this multi-alleleic example, the start of the
reference matches this particular alternate allele, so needed to be
checked as well). I've put a fix in branch 73
TranscriptVariationAllele.pm to improve HGVS compliance here.

Thanks for reporting this one - I'm sorry to hear it was such a pain
to pull out!

All the best,

Sarah




More information about the Dev mailing list