ExAC MAF above 30% not identified in 100Genomes

[jorgebm]

There are some SNP with high MAF frequencies on ExAC that are not identified in 100Genomes project. 1000G project aims to identify variants with frequencies of at least 1% in populations studied. However, ExAC has identified variants with MAF above 30% (consistent in all populations) that are not identified in 100Genomes.

They seems to be not just a few exceptions. Two examples,

rs1052422

ExAC MAF freq is abou 30%. This freq. is consistent in different populations. It is not in paralogous.

rs55796947

ExAC MAF freq is abou 30%. This freq. is consistent in different populations. Suspiciuous to be in paralogous.


Do you know how to explain such kind of SNP (MAF high freq. in all populations) not be in 1000G but ExAc?. I am filtering out MAF above 1% looking for a causal variant in mendelian disease. I am not sure if I should trust 1000G or ExAC for such variants (high MAF in ExAC not in 1000G).

Any suggestion?

Thanks

[Richard Finney]

There's a 1000 genomes "blacklist".


zcat chr2.bed.gz | awk '{if (($2<=130949553)&&($3>=130949553)) print $0}'
chr2 130949531 130949598 pilot

zcat chr17.bed.gz | awk '{if (($2<=21204210)&&($3>=21204210)) print $0}'
chr17 2120376321204683 pilot

[jorgebm]

Thank you , Richard.

Are you referring to mask "accessible" genome done by 1000G?.

An so, are ExAC safely addressing MAF in such regions?.


Thanks again!!!.

Best

[Richard Finney]

Clarification: I actually don't know if the files suppliekd by 1000 genomes is a whitelist or a blacklist.
I just wanted to point out that a possible reason that Exac and 1000 genomes are different is things like the 1000 genomes black list.