Very low allele frequencies in chrX of gnomad4.1 Joint

General
1

I am looking to filter out common IKBKG variants (found in chrX). I downloaded the gnomad.joint.v4.1.sites.chrX.vcf.bgz file and extracted only the IKBKG variants where AF_joint > 0.1 with the below command but I only got 8 variants. I believe the number of common variants is far too low. Could you look into this?

bcftools view -H -r chrX:154541179-154565047 -i 'INFO/AF_joint > 0.1' gnomad.joint.v4.1.sites.chrX.vcf.bgz

2

I am also seeing 8 variants with a joint AF > 0.1 using the joint frequency Hail Table.

Note that coverage across this gene is very low:

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