Population allele frequency

Question

[erzal.scarlett3]

Is it possible to calculate a population allele frequency for a novel variant? How?

[miles.anderson]

We'd probably need more information to help you. Is it an SNP? Have you already done the variant calling for your population? How many samples do you have? Is your VCF separated by population or does it include samples from multiple populations?

[erzal.scarlett3]

Yes, it's a SNP. This novel variant was identified in a single individual as a result of couple genetic screening (so only 2 samples have been screened for the presence of this variant). No population study is done. We want to report this novel variant, and one of the reviewer asked us to add PM2 criteria of the ACMG guideline for variant classification to change its current status from VOUS to likely pathogenic by describing the population allele frequency of this variant. Does it seem logical though since only 2 samples have been screened?