[ensembl-dev] possible VEP bug

Fiona Cunningham fiona at ebi.ac.uk
Wed Mar 21 15:54:33 GMT 2012


Hello,

Thank you for the information. That's what I thought. We will take a
look and make sure that the VEP is doing the correct thing here.

Best wishes,

Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612



On 21 March 2012 14:54, S Venkata Suresh Kumar
<suresh.surampudi at india.semanticbits.com> wrote:
> As for HGVS standards, For a transcript, -1 and +1 refer to one base
> upstream and one base downstream of coding region respectively.
>
> Regards
> vs
>
> On 03/21/2012 08:16 PM, S Venkata Suresh Kumar wrote:
>> Hi Fiona
>>
>> I guess you are right. As for HGVS standards, For a transcript, +1 and
>> -1 refer to one base upstream and one base downstream of coding region,
>> respectively.
>>
>> For eg.
>>
>> 1) CCDS6119.1:c.3327+1G>C means for this transcript (CCDS6119.1), one
>> base downstream (+1) to 3327th base is G (start of intron- first base of
>> intron is G) in reference and is substituted with C. This is a essential
>> splice site variation.
>>
>> 2) CCDS6119.1:c.3327-1G>C means for this transcript (CCDS6119.1), one
>> base upstream (-1) to 3327th base is G (end base of intron- last base of
>> intron is G) in reference and is substituted with C. This again is a
>> essential splice site variation.
>>
>> Please do correct me if I am incorrect.
>>
>> Regards
>> vs
>>
>> On 03/21/2012 07:53 PM, Fiona Cunningham wrote:
>>> Hello Sarah,
>>> I think you have the most recent  HGVS knowledge. Does what he says
>>> makes sense? What happens to HGVS when you are on the opposite strand?
>>> Presumably it is all relative to the transcript.?
>>> Fiona
>>>
>>> -----------------------------------------------------------------------------------
>>> Fiona Cunningham
>>> Ensembl Coordinator, Ensembl Variation Project Leader.
>>> EMBL-EBI, Genome Campus, Hinxton, UK
>>> www.ensembl.org || www.lrg-sequence.org
>>> fiona at ebi.ac.uk   || t: +44 1223 494612
>>>
>>>
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Michael Krauthammer <michael.krauthammer at yale.edu>
>>> Date: 21 March 2012 01:25
>>> Subject: [ensembl-dev] possible VEP bug
>>> To: dev at ensembl.org
>>>
>>>
>>> A possible (small) VEP bug report:
>>>
>>> The HGVS input parser does not seem to check for the directionality of
>>> the transcript
>>>
>>> The following (correct) input:
>>>
>>> CCDS6119.1:c.3327+1G>C
>>>
>>> results in error.
>>>
>>> The following (wrong) input works:
>>>
>>> CCDS6119.1:c.3327-1G>C
>>>
>>> The output of above input results in
>>>
>>> CCDS6119.1:c.3327-1G>C  8:41552109      C       CCDS6119.1
>>> CCDS6119.1      Transcript      splice-5        -       -       -
>>>  -       -       -
>>> ENSP=CCDS6119.1;HGVSc=CCDS6119.1:c.3327+1G>C;INTRON=28/41
>>>
>>> Nota bene: GVSc=CCDS6119.1:c.3327+1G>C  (!) which is the correct notation.
>>>
>>> Michael Krauthammer
>>>
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