Tollaly confused about finding variants allel frequencies.

Question

[amir.jebelli]

Hi,

I checked a few variant allele frequencies but I got different result from different websites. I checked my variances in NHLBI Exome Sequencing Project (ESP) and also check with this site from System Biology.

For example for the following variance I got MAF = 0.43 from ESP and MAF < 0.01 from Kaviar!

Can anybody tell me the popular and academic accepted way of reporting allele frequency in papers?

Answer 1

[Cyriac Kandoth]

You can run your variants through Ensembl's VEP, which reports the following columns (as of VEP v81)

GMAF - Non-reference allele and frequency of existing variant in 1000 Genomes
AFR_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined African population
AMR_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined American population
ASN_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined Asian population
EAS_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined East Asian population
EUR_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined European population
SAS_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined South Asian population
AA_MAF - Non-reference allele and frequency of existing variant in NHLBI-ESP African American population
EA_MAF - Non-reference allele and frequency of existing variant in NHLBI-ESP European American population

[amir.jebelli]

Hi, Cyriac

I checked My variants in ensemble but all MAF fields are filled with - unfortunately no value reported there. You can see my result here on Ensembl.