I decided to have a look where the two SNPs only found in African populations that my mother has, come from in Africa. Using the SPSmart browser, I was able to check against individual African populations, rather than just the continent as a whole.
For the first SNP rs11224346 T didn't show up in Mbuti Pygmies, Kenyan Bantu or Namibian San, they all got C/C just like 100% of Europeans and Asians. The following populations did get T (I think as C/T or T/T):
Senegal Mandeka 0.04%
South African Bantu 0.06%
Nigeria Yoruba 0.07%
Even within Africans it seems rare but I am amazed that two out of the three populations who do have T are on the West Coast. According to Wikipedia, between the 16th and 18th centuries, almost a third of the Mandeka were shipped to the US and they suggest a significant portion of African Americans are descended from the Mandeka. Similarly, Wikipedia states that out of the 45 distinct ethnic groups taken to the Americas during the slave trade, at number 8 are the Yoruba of southwestern Nigeria.
Having a look on the NCBI website only the Nigeria Yoruba get T/T.
Within the 227 Yoruba people from Nigeria that were tested 80% got C/C, 18% got C/T and 2% got T/T which gives you an idea of how rare it is!
Interestingly, 25% of African Americans from SW America get the C/T combination with the rest getting C/C.
The other SNP rs17130316 appears to be rare but common across Africa. The highest score is the South African Bantu at 31% getting an A (I think this includes A/G and A/A), followed by the Kenyan Bantu at 22%, Senegal Mandeka 18%, Nigeria Yoruba 16%, Namibia San 10% and Biaka Pygmy 4% (A is not found in Mbuti Pygmies).
According to NCBI, African Americans and the Nigerian Yoruba are the highest getting 0.02% and 0.03% A/A respectively.
Could this be something to do with having ancestry from the west coast of Africa?
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