Checking the mitochondrial DNA using the raw data provided by 23andme I noticed that there were a few Leber's Optic Atrophy variants tested for. This disease does not always present if someone ends up inheriting the pathogenic allele (or alleles) but it is important to know if you're a carrier. The following are a few variants tested for:
rs1599988, with C being the risk allele
i5000099 (aka rs199476112 from what I gather looking at the position) = A
i3001205 (aka rs200855215) = G
i4000834 (aka = rs199476104) = C
It may be possible that there are miscalls in the raw data that 23andme provides. One way to check is to see how many people on OpenSNP have the risk allele. If it seems like a lot compared to the MAF (frequency) reported on dbSNP, then the genotype may be miscalled by 23andme. Sometimes that is not enough to know for sure, as 2% of the people on OpenSNP have a G for i3001205. Is that a lot of people or are those genotypes correct?
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