[ensembl-dev] Variation differences in NCBI vs Ensembl

[Will McLaren]

Hi Gavin,


On 1 March 2011 10:49, Oliver, Gavin <gavin.oliver at almacgroup.com> wrote:
> Hi all,
>
>
>
> Why would differences occur between NCBI and Ensembl in terms of variations
> existing for a transcript.
>
>
>
> For example NCBI sequence NM_006712 corresponds to Ensembl transcript
> ENST00000297532.
>
>
>
> When I retrieve related SNPs via NCBI and Ensembl separately the results are
> broadly similar however there are a few differences.
>
>
>
> For example NCBI shows rs1130560 but Ensembl does not.

This SNP has been failed by the Ensembl QC process, as you can see if
you search for the SNP identifier:

http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=7:150773617-150774690;v=rs1130560;vdb=variation;vf=2124870

Failed SNPs do not appear by default; you can view them by searching
for their identifiers, or by turning on the "Failed variations" track
on the location view.

>
>
>
> Whereas Ensembl shows rs117650642 whereas NCBI does not.
>

I can't answer this - the dbSNP page shows a consequence for this SNP
and transcript:

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=117650642

You'd have to ask NCBI why it doesn't appear in the view you are using!

Thanks

Will McLaren
Ensembl Variation

>
>
> Looking at variations is pretty new to me so I’m just trying to gain an
> understanding of why these differences might arise and how I should deal
> with them.
>
>
>
> Thanks in advance,
>
>
>
> Gavin
>
>
>
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