Extracting LOF variants and incidence from GnomAD for a list of genes
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3 months ago
amy__ ▴ 160

Hi all,

I have a list of around 200 genes which I would like to observe in GnomAD v3.2.1 I want to see the general trend of LOF tolerance and homozygote knockout tolerance (subjectively through the incidence and frequency of either LOF variants in the gene or the incidence of homozygote LOF).

I am aware of this post How extract data from gnomAD for some genes? and this package https://github.com/KalinNonchev/gnomAD_DB, however I am not sure if these are what I am after.

My overall aim is to be able to subjectively say which genes are likely to tolerate LOF heterozygotes (i.e does the gene have many LOF heterozygote variants in high incidence) or is the gene tolerant to LOF homozygotes (i.e does the gene have LOF homozygotes in high frequency and incidence).

Making these assumptions I can do, but ideally I would need a list of the LOF variants in these genes and their incidence in GnomAD.

Sorry to sound confusing! Does anyone have any ideas?

Thanks! Amy

Gnomad LOF genes • 199 views
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for the first question, the tools that predict haplo(in)sufficiency are fairly good now, and are integrated into standard (clinical) workflows already. for instance, you can check out clingen for genes of interest, then look at pHaplo or what have you.

for the LOF variants, we cannot help you without further information. wed need to know, specifically, what forms of, and level of, evidence you accept as proof that a given variant produces a LOF.

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