MAF in gnomAD

[somayehbakhtiari]

Hi, I have used AnnotSV v3.4 to annotate copy number variants identified through the GATK-gCNV pipeline. I need to filter these variants based on their frequency in gnomAD, but can find such information in the annotated file. Your help would be much appreciated!

[lgmgeo]

Hi Somaye,

Thank you for your interest in AnnotSV.

According to the ACMG technical standards (Riggs et al., 2020), a SV completely contained within an established benign CNV region would be classified as benign (if sharing the same SV type). => In this aim, AnnotSV searches for benign genomic regions completely overlapping the SV to annotate. Benign regions are selected from different sources:

For example, the method to extract benign SV from gnomAD:

So, to filter out benign DUP, you can use: B_gain_AFmax: Maximum allele frequency of the reported benign gain genomic regions (if available)

And to filter out benign DEL: B_loss_AFmax: Maximum allele frequency of the reported benign loss genomic regions (if available)

Another way is to specifically analyse the CNV with ACMG_class = 5 or 4.

Best,

Véronique