Chromosome position mismatch for SNPs in dna tests

Question

TL;DR: why is the position reported by DNA testing companies for an SNP on a particular chromosome different than the one in dbSNP/SNPedia databases?

I'm analyzing the raw DNA exports for the same person from 2 different companies.

There is, as expected, a small number of discrepancies on the genotype reported.

Strangely, there is also a (smaller) number of discrepancies on the chromosome and position reported for the same SNP (about 0.02% of the rs-ids that are common to both exports).

Trying to find out who is right, I looked at SNPedia and dbSNP. To my surprise, while SNPedia and dbSNP (logically) agree on the positions, they never seem to match the positions reported in the raw DNA exports.

While the two companies that I used agree on the position in the vast majority of SNPs, they are apparently always different from dbSNP. In 75% of the 101 differences between the two companies, the position number only differs by 1.

I'm surprised by this and I feel that I'm missing some underlying piece of information.

What can explain these differences?

Does the "position" in the DNA exports from 23andme and MyHeritage represent some other biological property than the position reported by dbSNP/SNPedia? Or is there a conversion formula? Or is the information from the exports unreliable?

Answer 1

Most or all consumer DNA companies doing autosomal SNP tests deliver their raw data (at least by default) based on human reference genome build 37 (GRCh37). This is effectively the standard for this arena because it is compatible with existing files and other companies, allowing matching and other processing. dbSNP and SNPedia have changed to use the next major genome update, build 38 (GRCh38). The major genome builds can be expected to have different position numbers for most all comparable places in the genomes, including of course all SNPs which are defined in both builds (most of them).

So the differences in positions shown in your raw data files and dbSNP/SNPedia are due to this difference in the reference builds they are based on. I don't know a way of getting build 37 positions on SNPedia, but on dpSNP one way of seeing the build 37 position is to scroll down to "Genomic regions, transcripts, and products", "Choose placement" of GRCh37, and then hover over the blue highlighted SNP name, which will show a drop-down list with the (build 37) position, among other things.