# Missing variant?

**URL:** <https://discuss.gnomad.broadinstitute.org/t/missing-variant/859>\
**Category:** Methods\
**Created:** [September 20, 2026, 5:51pm UTC](https://discuss.gnomad.broadinstitute.org/t/missing-variant/859 "2026-09-20T17:51:01Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![JAb](https://sea2.discourse-cdn.com/flex016/user_avatar/discuss.gnomad.broadinstitute.org/jab/32/394_2.png) [@JAb](https://discuss.gnomad.broadinstitute.org/u/JAb)\
**Post date:** [September 20, 2026, 5:51pm UTC](https://discuss.gnomad.broadinstitute.org/t/missing-variant/859/1 "2026-09-20T17:51:01Z")

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Hi there,

Could someone please explain to me why SNV [12-51916114-T-G](https://gnomad.broadinstitute.org/variant/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!

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**Author:** ![kchao](https://sea2.discourse-cdn.com/flex016/user_avatar/discuss.gnomad.broadinstitute.org/kchao/32/6_2.png) [@kchao](https://discuss.gnomad.broadinstitute.org/u/kchao)\
**Post date:** [September 23, 2026, 8:51pm UTC](https://discuss.gnomad.broadinstitute.org/t/missing-variant/859/2 "2026-09-23T20:51:23Z")

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The variant [12-51916114-T-G](https://gnomad.broadinstitute.org/variant/12-51916114-T-G) has an [AC0 flag](https://gnomad.broadinstitute.org/help/what-do-the-flags-on-the-browser-mean):

 ![image](https://us1.discourse-cdn.com/flex016/uploads/broadinstitute1/original/1X/e4cf044b49b37c3382a229815187102ce52462eb.png)  
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.