[ensembl-dev] possible VEP bug

[Sarah Hunt]

Hi Michael,

Thanks for reporting this problem. We have now improved support for
parsing intronic variants from HGVS nomenclature. The fix has been
added to branch-ensembl-66 if you would like to pick it up  ( the
changed file is
ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm).
Further modifications to how HGVS annotation is output, taking into
account other recent messages on this list, will be coming in release
67.

As ever, do let us know if you see further discrepancies we can
address. Specific examples we can add test are particularly valuable.

Best wishes,

Sarah

On Wed, Mar 21, 2012 at 3:54 PM, Fiona Cunningham <fiona at ebi.ac.uk> wrote:
> 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
>>>>
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> List admin (including subscribe/unsubscribe):
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/