best practice to choose AF threshold based on population number

Question

[prasundutta87]

Hi,

What is the correct way or best practice to choose allele frequency thresholds to separate rare from common variants when your cohort is less than 100? Additionally, does AC or AN need to be taken into account for this?

Regards,
Prasun

[4galaxy77]

Why do you need to classify a variant a ‘rare’ or ‘common’? What’s your end goal?

[prasundutta87]

I am only interested in rare variants (SVs in my case) because if they are common in my population, their effect will be benign/not pathogenic with respect to a family. My cohort is <100.