SNPs in this table we're previously part of the #Livewello standard report, but with version 2.0, they have been removed because they have ambiguous RefSNPs, which makes it difficult to accurately determine their minor allele.
MNPs: Some SNPs on dbSNP are listed with three RefSNP alleles instead of two. SNPs should only have two alleles (refSNP alleles). One on the plus strand and another on the minus strand.
After talking to a representative at NCBI about why some SNPs have 3 alleles, Livewello’s Founder was told that these types of SNPs are considered ambiguous because they can have variations in more than one nucleotide. In fact they aren’t really SNPs, but rather MNPs (Multiple Nucleotide Polymorphisms) For example rs1611430 refSNPs are reported as A/G/T (see explanation on NCBI FAQ: http://www.ncbi.nlm.nih.gov... ).
Strand orientation: SNPs list on dbSNP, as on 1000Genomes and most genomic services, are listed on the forward strand. When the RefSNPs are reported on the minus strand, the expectation would be that one or both of the RefSNPs would be a complementary allele to the minor allele. When this is not the case, these SNPs are also considered ambiguous.
The deleted SNPs can be found in the SNPs library:
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