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Allele discrepancy between Database and Publication

Dear community,

I'm interested in to genotype the SNP rs679620, however in Ensembl (and the Lab Kit Provider) the reference/alternative alleles for the forward strand are T/C, whereas in the publication the alleles are A/G.

How may I interpret this discrepancy? Should I expect to look for the C allele, which in the reverse strand is actually a G?

Thanks in advance for your suggestions,

snp genotype ensembl dbsnp
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updated by Emily Emily • written by snp_guy • snp_guy

1 answer

Strand. The databases will always quote the forward strand alleles, papers quote either, often the strand that the gene they're interested in is on, and no, they often won't tell you which one.

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written by Emily Emily

Thanks for your quick reply Emily.

So this assumption is correct: "Should I expect to look for the C allele, which in the reverse strand is actually a G?"

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written by snp_guy • snp_guy

In your genotyping results, yes.

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written by Emily Emily

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