Missing variant?

Methods
1

Hi there,

Could someone please explain to me why SNV 12-51916114-T-G is present in gnomAD v4.1.1 (allele count 0) but 12-51916114-T-C and 12-51916114-T-A in the same nucleotide are not?

Thanks!

2

The variant 12-51916114-T-G has an AC0 flag:

image
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This means that at least one sample in the gnomAD dataset had a non-reference genotype call for this variant, but the non-reference genotype call(s) did not pass our genotype quality filters (described in the image above; GQ < 20; DP < 10; and AB < 0.2 for het calls).

If the other variants at the same locus are not present in the dataset, that means no gnomAD samples had a non-reference genotype pre- or post- genotype filtering.