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

[Jose M. Gonzalez]

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