Allele Frequency Thershold

Question

[786]

Hi I'm retrieving my results through annovar as it gives more compiled results. I found here the allele frequency calculated through 1000 Genome Browser but I'm confused here how to pick the rare variants from here I'm working on SAS population what threshold of frequency I should set to pick up the rare variants of this population or there is no need to set a threshold to find risk associated variants from here??

Answer 1

[Denise CS]

I feel that the definition for common versus rare variants can be quite arbitrary. In Ensembl, we've chosen 1%. So a variant with a frequency of 1% or higher is deemed to be common. You can run the VEP (Variant Effect Predictor) to annotate your variants, exclude the common ones through the filtering options (you can choose the threshold you want) and get pathogenicity predictions in addition to clinical significance of the variants, association to diseases and/or other phenotypes and plenty more.

[786]

thank u so much.Did you mean that there is a need to set a threshold?