[ensembl-dev] [VEP] Bogus annotation in variant from Cosmic

[João Eiras]

On 30 January 2017 at 15:06, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hi Joao,
>
> The variant you describe overlaps one base of an intron and four bases of an
> exon. This exon in the transcripts you describe does not form part of the
> coding sequence, and is upstream of the start site, so forms part of the 5'
> UTR, hence why the variant is annotated as a 5' UTR variant.
>

Ah, I got confused, thought for a second splicing sites would occur
only in the CDS (not used to seeing long 5 UTRs).

Then two follow up questions, why is cdna_start==cdna_end ? Because of
it affecting the splicing site ? I'd expect it at least to be
cdna_start == 221 and cdna_end == 224.

And, given the TranscriptVariationAllele how can I get the
transcript's cds start offset in relation to the cdna ?

Thank you !