Is there any good prediction tools that can predict deliriousness of nonsense variants?
Im trying to prioritize germline variants that might be potentially pathogenic to the disease that I'm investigating. After filtering for rare variants, and my genes of interest, i still have quite a number of nonsense variants.
When I check some of the nonsense variants, the stop codon is gained not too far away from the canonical stop codon and thus it "might" be less deleterious as compared to a stop codon that is gained near a start of a transcript?
I came across dbNSFP database and I could see some tools could predict deleteriousness of nonsense variants such as MutationTaster, LRT, FATHMM etc. How reliable are these prediction tools ?
Some of nonsense variants are indeed non-pathogenic but how can I predict deleteriousnesss for unknown nonsense variants?