Some structural variants in gnomAD SVs v4.1.0 such as DUP_CHR8_77D3CCE7, DUP_CHR8_0DFC84AB, and DUP_CHR8_5D05B234 show detectable allele counts in the population data. However, the database also indicates homozygous individuals for the variants at an unexpectedly high frequency. Is there any proof of the homozygosity in the individuals with homozygous variants? Is the homozygosity assumed by the read depth only?
You might want to take a look at the concluding part of this thread… that I started a while ago, in a related issue. It seems that such entries might represent triplications, rather than dups.
Hi,
Thank you for the question. Please see attached as the sequencing depth distribution of the 3 duplication. y-axis represents the relative copy number against null (copy number =2), so that y=1.5 indicate 3 copies, y=4 indicate 4 copies etc.
You are correct that we cannot differentiate samples with 4 copies between heterozygout vs. homozygout, as we did not phase these SVs. the homozyoug genotype were assigned based on copy number.
Best,
