[ensembl-dev] unmapped/un-displayable SNP from dbsnp

Bert Overduin bert at ebi.ac.uk
Fri Oct 8 16:10:31 BST 2010


Although it says on the mentioned dbSNP page:

RefSNP Alleles:	A/G

it also says:

NM_021964.2:c.1749G>A
NM_021964.2:c.1749G>C
NM_021964.2:c.1749G>T

and further down on the page it again says:

CCG => CCA
CCG => CCC
CCG => CCT

But the in the Population diversity part again only A and G are
mentioned as alleles.

So, I get the feeling dbSNP is messing up things here ....

Cheers,
Bert


On Fri, Oct 8, 2010 at 3:54 PM, Kim Brugger <kim.brugger at easih.ac.uk> wrote:
> Hi
>
> If you look at the dbsnp page for this snp it is only two alleles A/G for
> this snp, so it looks like the counting of alleles is faulty. Furthermore
> the SNP is represented in the 1000 genomes data, and other datasets I deem
> trustworthy.
>
> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1053738
>
> Thanks for explaining how/why this filtering is done.
>
> Cheers,
>
> Kim
>
> On 08/10/10 14:14, Graham Ritchie wrote:
>>
>> Hi Kim,
>>
>> This SNP has *more than* 3 alleles, and we have taken the decision to fail
>> all such SNPs, we debated this decision internally recently and Paul
>> concluded as follows:
>>
>> "These are still far, far more likely to be errors than real.  While some
>> probably exist, true SNPs with all four alleles require very complex
>> selection pressures to remain in the population and so this number is simply
>> never likely to grow to "many SNPs."  In fact, the word quadallelic does not
>> return any results in Pubmed.
>>
>> This does not mean that it will never happen, only that it is very, very
>> rare.  Note that we don't fail triallelic SNPs, which are also rare and
>> enriched for error."
>>
>> Hope this makes sense. If you have example of SNPs that don't appear for
>> other reasons then please let us know. We do track all SNPs we fail and the
>> reason for doing so in the failed_variation table of the variation database.
>>
>> Cheers,
>>
>> Graham
>>
>>
>> On 8 Oct 2010, at 13:54, Kim Brugger wrote:
>>
>>
>>>
>>> Hi
>>>
>>> I am looking for the rs1053738 snp. When I do a search on the ensembl-web
>>> it is found and it exists with 2 synonyms, but if I want to display I am
>>> told it was not mapped as the variation has 3 alleles.
>>>
>>> The SNP should be located at  3:124951820-124951821. I have a large set
>>> of snps that I cannot find either with the ensembl-web or using the api.
>>>
>>> Cheers,
>>>
>>> Kim
>>>
>>> --
>>> ==========================================================
>>> Kim Brugger
>>> EASIH, University of Cambridge
>>> www.easih.ac.uk
>>> ==========================================================
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>
>>
>>
>
>
> --
> ==========================================================
> Kim Brugger
> EASIH, University of Cambridge
> www.easih.ac.uk
> ==========================================================
>
>
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> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
>



-- 
Bert Overduin, Ph.D.
PANDA Coordination & Outreach

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert




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