[ensembl-dev] possible VEP bug

S Venkata Suresh Kumar suresh.surampudi at india.semanticbits.com
Wed Mar 21 14:54:16 GMT 2012


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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