GNOMAD exome vcf field missing? number of hemizygous individuals

Question

[brismiller]

Hey everyone,

I am searching the GNOMAD 2.1.1 exome vcf and I am having trouble finding a field that I am interested in. I am looking for the number of individuals that are hemizygous for that variant.

For genes that the variant is on a non sex chromosome, this information is easy to find, but not for variants on the sex chromosomes.

e.g. The number of individuals can be found in the field "nhomalt". For example look at the gene https://gnomad.broadinstitute.org/gene/ENSG00000117475?dataset=gnomad_r2_1 , you can see on the right that the number of homozygotes is shown.

Sadly though I cannot find the field that corresponds to the number of hemizygotes.

Any suggestions?

Thanks in advance, this is my first time using GNOMAD

Answer 1

[rbagnall]

Lets look at a gene on the X chromosome, say F8

There is a variant at X-154065843-G-A, which is found in 103 males in the exome data and 92 males in the genome data, giving a total of 195 males who have this variant and are hemizygous.

Now lets get the male allele count (thus number of hemizygous males) from the gnomad exome VCF file. Specifically, we want the annotation called AC_male, which is the count of male with the variant.

tabix https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.X.vcf.bgz X:154065843-154065843 | tr ';' '\n' | grep '^AC_male'

This returns AC_male=103, which is the number of hemizygous males who have this variant in the exome VCF.

[brismiller]

Thank you! That was exactly what I was looking for.