[ensembl-dev] possible VEP bug

[S Venkata Suresh Kumar]

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/
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0xEC5BC523.asc
Type: application/pgp-keys
Size: 1744 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120321/b082c892/attachment.bin>