Population AF versus gnomAD AF

General
1

Hi,

I have made a cohort of patients via UK biobank and I explored variation within a given genomics coordinates; The results have columns as below

Cohort AF Cohort Allele Count Population AF Population Allele Count GnomAD AF

Variant ID	Chr	Position	RSID	Reference	Alternate	Type	Cohort AF	Cohort Allele Count	Population AF	Population Allele Count	GnomAD AF
7_140479093_T_A	7	140479093	["rs879754601"]	T	A	SNP	0.00044677	7	0.000484213	455	
7_140479112_C_T	7	140479111	["rs985170766"]	GC	GT	SNP	0.000127649	2	0.000101099	95

What is the difference between population allele frequency and gnomAD allele frequency

2

Hello and thank you for reaching out - unfortunately though this is a question for the UKBB team. We are not responsible for making the AFs that are annotated in UKBB data, and we don’t use the same titles as they use. The UKBB team is using our data for this, but you’d have to go to them for how they’re slicing/formatting/naming it, so your questions should be directed towards their team or their docs. Hope the search goes well and you get a clear and concise answer soon!

3

Thanks I will ask their support. Please, could you help me with this question
Today, I noticed something which I want to share here:

I extracted mutations in these coordinates

7:140476600-140480852

7:140922446-140926601

7:141013033-141016000

7:141550400-141552801

7:141736785-141740201

from gnomAD non_cancer_nfe & gnomAD biobanks_nfe sub populations, independently, but I have not been able to figure out how I got the same number of mutations from 16k controls_and_biobanks_nfe and 74K non_cancer_nfe from gnomAD

Any idea please?

Thank you in advance.