Unusual issue with common SNV assigned low PSAP p-value

[dconrad]

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.

[martiliasf]

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?