[ensembl-dev] [VEP] Bug stripping REF/ALT alleles ?

[João Eiras]

Hi.

I stumbled upon COSMIC annotation COSM366465
http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=366465

The annotations is in the VCF as

chr4 46977409 COSM366465 CCT CAT

VEP annotates this as (splice_region_variant,coding_sequence_variant)
over transcript ENST00000264318. This transcript is in the reverse tr

However, this is actually a SNP in the last nucleotide.

The variant can be stripped as

chr4 46977410 COSM366465 C A

and in this case VEP does annotate it as a missense_variant.

Without looking at the code, my guess is that VEP strips the common
nucleotides of he tips of REF and ALT from the left in case of a
forward strand transcript, and right side in case of a backward strand
transcript. So, the left most C remains there and VEP thinks that
nucleotide is changed.

Am I missing something ?