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I am combing through my 23 & me raw data and I am a little confused on SNP terminology. I am using NCBI's genome browser and SNP database. As an example we can all follow here is a link to a CYP1A1 SNP https://www.ncbi.nlm.nih.gov/snp/rs28399430. When you open this link you will see alleles listed as G>C. Which one of these is the reference genome and which is the pathogenic allele? Is the relationship always constant (like in x>y, x is always the reference and y is the substitution). If you scroll down to the genome browser view, there also doesn't appear to be any way to tell + vs - sense strand (ie making it difficult to tell G for C mutations or vice versa). I would just assume its the top strand? The ultimate goal here is for me to look through 23&me and compare my SNP genotype to the reference genome and see if my genotype exhibits pathogenic SNPs in certain genes.

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  • $\begingroup$ > "Which one of these is the reference genome and which is the pathogenic allele?" How have you concluded that the less common, non-reference allele is pathogenic? I don't see any clinical data for that $\endgroup$ – swbarnes2 Apr 10 at 20:37
  • $\begingroup$ For specific examples I’m looking at it’s the case. Not globally- should have made my self clear sorry $\endgroup$ – Joe Apr 10 at 22:28
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Quick answer is yeah, the G is the "reference allele" as you put it. The greater than symbol is acting as an arrow, ie, G goes to C, that is, G is replaced with C.

Actually you get a pretty clear indication of that if you look down a line it two where it mentions the frequency:

C=0.000419 (104/247982, GnomAD_exome) C=0.000494 (62/125568, TOPMED) C=0.000538 (62/115296, ExAC)

The C frequency is way too low to be the "normal" allele. It's rather the substitution which results in a missense variant. You can see more specific stats by clicking on the frequency button. In this case they basically just say that in all studied populations the G variant is by far the most common.

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