[ensembl-dev] VEP - start_lost consequence on first codon of transcripts with incomplete CDS 5'

[Will McLaren]

Thanks Jose and Cyriac.

This will be fixed in the next VEP release.

Regards

Will McLaren
Ensembl Variation

On 8 June 2016 at 18:23, Cyriac Kandoth <kandoth at cbio.mskcc.org> wrote:

> Keeping variant consequence separate from the quality of the transcript,
> neatly limits the complexity of VEP. A solution for you, might be to pick
> and report the consequence of the variant on the "canonical transcript". Or
> maybe the transcript that is actually expressed in the tissue you're
> studying. This is they motivation behind the --pick and --pick-order
> options in VEP:
>
>
> http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_pick
>
> ~Cyriac
> On Jun 8, 2016 6:37 AM, "Jose M. Gonzalez" <jmg at sanger.ac.uk> wrote:
>
>> Hi,
>>
>> We have noticed that VEP calls a "start_lost" consequence on variants
>> affecting the first codon of transcripts with an incomplete CDS 5', i.e.
>> those tagged with a 'cds_start_NF' attribute. In most cases this first
>> codon is not even a canonical start codon. Here is an example:
>>
>> http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000116198;r=1:3829193-3829524;t=ENST00000461667;v=rs763522630;vdb=variation;vf=129057128
>>
>> These are partial transcripts for which the true start codon is not
>> known, so we believe that a "start_lost" consequence does not seem
>> appropriate in this case. Perhaps a consequence such as "missense_variant"
>> or "synonymous_variant" would be more adequate for variants falling on
>> these codons.
>>
>> Would it be possible for VEP to handle transcript attributes indicating
>> partial length in order to call these types of consequences more accurately?
>>
>> Thanks,
>> Jose
>>
>> --
>> Jose M. Gonzalez
>> Senior Bioinformatician - GENCODE
>> HAVANA Team
>> Wellcome Trust Sanger Institute
>> Hinxton, UK
>>
>>
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