Synonymous Mutations And Their Effect On Splice Site.

Question

[Omid]

Hi To analysis exome sequence data sometimes people exclude synonymous mutation.BUT it might affect on splice sites depend on how far it is from splice sites.

I have a list of synonymous variants.What is the easiest way to analyze these kind of mutations.I mean an on line web page where I upload my variants list and have a batch output.Thanks

[Vikas Bansal]

Hi. How did you call these synonymous variants? If you used PolyPhen etc., I think it would have told you if the mutation is splice site mutation.

Answer 1

[ff.cc.cc]

"Ensembl provides the facility to predict the functional consequences of known and unknown variants using the Variant Effect Predictor (VEP)"

Try VEP here.

[Omid]

Thanks.I tried VEP for 44 synonymous variants but that sounds in these variants we do not have SIFT or PolyPhen prediction in VEP.