Hello,
I’m trying to better understand the reliability of allele frequencies in the gnomAD database from a variant curation perspective. Many genes have pseudogenes, and I was wondering if there is some quality metric assesses the likelihood that a variant entry in gnomAD could include pseudogene instances.
For example, in my laboratory, we detected gnomAD in a patient. However, the call had mapping quality of 0 (MAPQ0) in our patient, bringing pseudogene detection/interference into question. Thus, I wondered if any of the 24 heterozygotes in gnomAD could represent detection of the variant on a pseudogene and consequently be inflating the MAF and FAF calculations for this variant. What could I check on the variant page to help me rule in/out pseudogene interference with the counts?
Thanks in advance for any guidance!
NM