Hi,
I have a list of variants (from whole exome sequencing), I would like to narrow these down to the significant ones only.
Is VEP Impact the best factor to look at? i.e. should I only look at the 'HIGH' impact variants.
Or is there a different/ accepted practice?
Thanks.
•
written
by
nub6 •
1 answer
A general approach for variant annotation/classification would be something like this:
1- Based on the pattern of inheritance, select homozygote or heterozygote variants.
2- Filter out variants based on data from the population frequency databases like GnomAD, KAVIAR, 1KG, GME, HRCR1 ...
3- Filter out variants based on bioinformatics tools that assess a variant impact on the protein like CAD, VEP, metaSVM, and...
4- Checking clinical databases ( like ClinVar) for the variant.
5- Querying HPO with a list of genes and your phenotype terms. You can do this online with tools like Phenolyzer
6- Using ACMG recommendations for variant classification.
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