Dear gnomAD team, I noticed something weird regarding the AF between V2 and V4 (considering both genomes and exomes). The main problem is for the variant in gen CBS:c.699C>T (p.Tyr233Tyr), in v2 there is AF but in v4 there isn’t variant. This fact could affect to other variants… Why could it is happening?
Thanks a lot all of you for the hard work!!
The GRCh38 reference contains a false duplication of the CBS gene, which impacts alignment to and variant calling within this gene. The coverage profile of CBS in v4 reflects the difficulties in mapping to this gene:
For more information about false duplications in the GRCh38 reference, please see this paper.