Given a variant ID, is it possible to request it estimate population frequency?

Question

[mithrado]

Given a missense variant ID, is there a way (via a database or even flat file) to request its estimate frequency or some other importance metric?

By importance metric I mean: how common is this mutation in the average global population or how many times it happens for each 1000 individuals etc.

Thanks you in advance!

Answer 1

[Giovanni M Dall'Olio]

Of course, check the FAQs from the 1000 Genomes paper: http://www.1000genomes.org/faq/how-can-i-get-allele-frequency-my-variant

You can also use the --indv option in vcftools to select only the individuals belonging to a single population, to obtain the MAF only in that population.

[mithrado]

I will try this, but it does not cover somatic variants from CosmicDB, does it?

[Giovanni M Dall'Olio]

Exactly, that is the frequency only in germ lines. There is no much data on the frequency of somatic mutations in human populations, although you can get an estimate from the ICGC data portal.

Answer 2

[mikhail.shugay]

If it is an oncogenic somatic mutation, it could be too rare to be found in 1000 individuals. However the last solution suggested by Giovanni might work in your case