[ensembl-dev] Human MAF numbers

Laurent Gil lgil at ebi.ac.uk
Tue Jan 30 13:14:00 GMT 2018

Dear Beat,

We have some documentation in the Ensembl Glossary 
[https://www.ensembl.org/Multi/Help/Glossary?db=core] (not that easy to 

*- Global MAF (Global Minor Allele Frequency):*
Minor Allele Frequency (MAF) refers to the frequency of the second most 
common allele at the position where a sequence variant (such as a SNP) 
has been identified. In Ensembl, the global MAF is calculated using the 
allele frequencies across all 1000 Genomes Phase 3 populations.

We also display the "Highest population MAF", which corresponds to the 
highest MAF found in the main human genotyping projects we have in 

In the Ensembl REST VEP endpoint, this 1000 Genomes MAF correspond to 
the "minor_allele_freq" information.

Th|e "gnomad_maf" is calculated from the gnomAD VCF files (which 
provides allele counts and frequencies).|


|We will try to improve our documentation about the MAF in the next 
Ensembl release.|

||I hope this helps.||

|Best regards,

|| ||

Ensembl Variation

On 29/01/2018 16:16, Wolf Beat wrote:
> Hello,
> i have a question that i sadly could not find an answer in the documentation (but its likely somewhere, i just can't find it).
> For human variants there is a MAF number displayed on the website. It is usually written in a tooltip where this information comes from. But, if there are multiple MAF sources, how is the MAF choosen?
> I guess this question also applies to the VEP rest service, which sometimes (not always!) returns a "minor_allele_freq" information. From what i understand, thats the same as the one displayed on the website, but again, how is it calculated?
> I know that VEP also provides me with gnomad_maf etc. But that "Global" MAF Number is calculated how exactly?
> I'm sure this is documented somewhere, but i must have choosen the wrong keywords. Thank you for pointing me towards the correct information!
> Kind regards
> Beat Wolf
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