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

[Will McLaren]

There does seem to be a bug in the cdna coordinate reporting in the JSON
output, I'll take a look at this.

Assuming you have API access, you can get the CDS start and end relative to
the CDS from the transcript object [1]. From within a plugin, this would
look something like:

sub run {
  my ($self, $tva) = @_;

  my $tr = $tva->transcript;
  my $cds_cdna_start = $tr->cdna_coding_start();

  # etc
}

Regards

Will

[1] :
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#a9d16156942ffec6050cb9bbea340e370

On 30 January 2017 at 15:44, João Eiras <joao.eiras at gmail.com> wrote:

> 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 !
>
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