Dear members of gnomAD,
We are investigating structural variation in a repetitive region on human chromosome 15. In the SVs v4.1.0 database, we identified two sets of deletion variants - one comprising three calls and the other two - that span overlapping genomic intervals and show very similar allele counts across genetic ancestry groups (with identical homozygous counts). This pattern suggests that these variants may be genetically associated, however, because they delete overlapping/identical sequences, they should not be able to co-occur on the same chromosome, which raises the possibility of an annotation, merging, or representation issue.
Could you please check whether something might be going wrong in how these variants are represented or counted? The variants are:
DEL_CHR15_3430BA77; DEL_CHR15_8CD85032; DEL_CHR15_E92B2C3D
and
DEL_CHR15_1F817031; DEL_CHR15_2D64E68E
Thanks a lot,