Variant's authenticity in the V4 dataset

Thank you very much for the invaluable contribution you make with gnomAD. Your work is tremendously beneficial for those of us involved in diagnostics.

I would like to inquire about the 6-98835104-C-CG variant identified in the V4 dataset. I am keen to understand whether this variant is more likely a false negative or a genuine variant.

There is evidence suggesting that POU3F2 Loss of Function (LoF) variants are linked to a specific type of intellectual disorder. This particular variant is observed in 321 heterozygous cases, as it is predicted to result in a truncation of the protein. However, the frequency of this variant does not seem consistent with the prevalence of the associated disorder. Additionally, another variant at the same position (6-98835104-CG-C) is present in 28 heterozygous cases. The available reads in gnomAD suggest that this variant appears genuine, despite the challenging region for sequencing. Notably, both of these variants are absent in the V2 and V3 datasets.

In contrast, the next most frequent LoF variant in this gene, 6-98836151-C-CG, is found in 8 heterozygous cases and present in 1 heterozygous case in the gnomAD V3 dataset.

We recently encountered a case where a duplication was identified in a patient and subsequently confirmed by Sanger sequencing. Furthermore, these variants have not been commonly observed as false positives in our Whole Genome Sequencing cohort. Thus, I am left to wonder if they could potentially be false positives.

Thanks again for your help.

I would be concerned about this variant. The inserted G occurs within a series of repeated Gs which will be subject to stutter, if you look at the metrics on the graphs, the genotype quality is lower than what we typically see, the sequencing depth is lower than most exomes, the allele balance is much lower at only 25%, and there are a number of other variants at the same position that add or subtract Gs. So I would not trust this variant.

Dear Heidi,

Thank you very much for your prompt response and for the great work you do. Your insights on quality metrics have been very useful.