Open dconrad opened 7 years ago
The site is multiallelic.
http://exac.broadinstitute.org/variant/9-99699485-GA-G
http://exac.broadinstitute.org/variant/9-99699485-G-C
I don't know how PSAP handles these, but to help figure this out, can you please share the exact call from your VCF file?
We have seen, very rarely, a common variant being assigned a very low PSAP p-value. For instance, the variant Chr9 99699485 (hg19) in NUTM2G has ExAC frequency of 0.13 and PSAP p-value of 10^-6. Unclear what the source of this issue is.