[ensembl-dev] Human MAF numbers

[Laurent Gil]

Dear Beat,

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

*- 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 
Ensembl 
(http://www.ensembl.org/info/genome/variation/data_description.html#populations). 


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,
|

|| ||

Laurent
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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