Why Is The Snp Info Missing From Dbsnp ?

Question

[NB]

Hello,

In dbSNP some variants like rs71263230,rs28399500,rs52830374 do not have information for the amino acid substitution or function but when you upload the same variants in a tool like SNPnexus or Annovar you get some result.

This happens very often with my list of variants ( 1000 out of 3500). What can be the reason for this ? Is this problematic to include these variants for further analysis ?

Thank you

[Pierre Lindenbaum]

AFAIK dbSNP doesn't provide this information (?). Have you ever seen it in dbSNP?

[NB]

Yes, if you see for rs6702447 in dbSNP, under "GeneView" it gives the function, substitution accession ids... but for the SNPs mentioned above, there is no such info under "GeneView" in dbSNP.....

[Pierre Lindenbaum]

I see, thanks for pointing this.

Answer 1

[Jorge Amigo]

the reason is simply because you are thinking that GeneView is somehow a prediction track (and it really looks like it, I should say), but it isn't. the information shown under the GeneView section comes from text mining pubmed articles, and for that reason you may find or not information on that section depending on the existence of literature on that particular variant. what annotation tools like ANNOVAR do is to calculate the amino acid change by placing the variant in a particular transcript (in fact, if several transcripts contain that variant position, the amino acid change would depend on the transcript and you would have to describe them all unless you precisely know which transcript does that variant correspond to), but this is different from that the GeneView section seems to be there for.

[NB]

thank you for the info..