[ensembl-dev] Variation beyond the gene range

Sarah Hunt seh at ebi.ac.uk
Wed Dec 13 13:54:25 GMT 2017

Hi Mahmood,

It is not clear how you obtained the file you are refering to. If this 
is output from VEP, by default we report variants within 5000 bases 
upstream and downstream of a transcript, so check the consequence type 
reported. You can modify this distance with the --distance option in the 
script and with similar options through the web and REST interfaces.

Best wishes,


On 13/12/2017 13:11, Mahmood Naderan wrote:
> Hello,
> In the CVF file, I see the following positions for a gene called ZNF778
> 89,294,381
> ...
> 89,299,279
> 89,299,876
> ...
> However, according to the website (and also, the API I used), the
> start and stop numbers for that gene is  89,284,118 and 89,295,363
> respectively.
> What is that fault? The variation positions are beyond the range.
> Seems that there is mismatch here.
> Regards,
> Mahmood
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