Question

How to find the variant type, location and effects (synonymous/nonsynonymous)

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8.8 years ago

MAPK ★ 2.1k

I have about 100 of these SNPs (chr:position:REF:ALT) as shown below. I would like to know what type of mutation they are (coding,noncoding, synonymous/nonsysnonymous, UTR, etc.). What would be the easiest way to get that information?

chr7:101063260:A:G
chr11:118532376:A:G

variant-type SNPs • 2.3k views

ADD COMMENT • link updated 2.4 years ago by Ram 44k • written 8.8 years ago by MAPK ★ 2.1k

Ram · Answer 1 · 2016-01-31

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8.8 years ago

Sean Davis 27k

Try Ensembl VEP:

http://www.ensembl.org/Tools/VEP

There are many other possibilities.

ADD COMMENT • link 8.8 years ago by Sean Davis 27k

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Thanks Sean. I have tried VEP already, but I am not getting anything for these SNPs. Is it possible that the are unknown (since GATK has called them unknown)?

ADD REPLY • link 8.8 years ago by MAPK ★ 2.1k

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They do not need to be known for VEP to work. What genome version are your SNPs on? Did you double-check that you were using the correct version of VEP (knowing that the default is GRCh38)? I suspect that you have GRCh37 (hg19) data, so you'll need to use the GRCh37 version of VEP.

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.8 years ago by Sean Davis 27k

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Yes, I used GRCH37 which is the version I have.

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.8 years ago by MAPK ★ 2.1k

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I just tried your first SNP (the chromosome 7 one) and got back positive results (it is a missense variant in COL26A1). Perhaps double-check?

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.8 years ago by Sean Davis 27k