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

Graham Ritchie grsr at ebi.ac.uk
Fri Oct 8 14:14:42 BST 2010

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.



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
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