How to determine significance of a variant?
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9 months ago
nub6 ▴ 20

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.

VEP next-gen • 280 views
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4
Entering edit mode
9 months ago
Hamid Ghaedi ★ 1.7k

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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Thanks that is useful

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