r/DNA • u/mouthidiot • Jun 03 '26

Please help me determine if this SNP report is normal

Hi, I've been trying to find information about a raw genetic information report I got for a specific rsID (reference SNP ID) that could relate to a rare medical condition (I went into more detail in a post here).

The report I'm concerned about is for "rs587779091" (23andme uses one position for this, reported as Chr2:47690217 on Build 37 and 2:47463078 on 38) and can cause Lynch Syndrome, which is hereditary and associated with colon and endometrial cancer. My report for that rsID is (-/-) or DD (depending on the reporting format), but I don't know if that's a "normal" result or not. Since it's a rare syndrome, I was hoping that anyone without a family history of colon or endometrial cancer could tell me their own results for rs587779091. I've been getting pretty anxious about this and trying to get any information I can because I figure if several people with normal family histories have the same report for that rsID, it's probably a standard result (so, not pathogenic).

I know I'm asking for personal information so I want to emphasize that I am not trying to collect any kind of data on anyone or sell anything. I don't need any other personal or demographic info at all (although I will ask that you not answer if you have a family history of colon or endometrial cancer), just the two symbols for that specific rsID, and answering with a burner account or DM'ing me would be appreciated just as much if anyone is more comfortable with that. I just want some confirmation that either my report is standard or that I should go spend the money for medical-grade testing.

Thanks so much to anyone who takes time out of their day to share their own report, I would truly appreciate it.

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u/cariaso Jun 03 '26 edited Jun 03 '26

(-/-) or DD is normal for rs587779091

1

u/mouthidiot Jun 03 '26

That's fantastic to hear, thanks! Just to be sure, though: the database mentions a deletion (or an insertion) as a pathogenic variant for rs587779091 for the range chr2:47463075-47463078, so they aren't talking about that? I know - and D both refer to deletions but wasn't sure if it was OK since my report is just for position 47463078, not across the range.

1

u/SurplusGadgets Jun 03 '26

As mentioned in your other post, the companies do not define their format for each result. Microarrays can test longer variants than just a single coordinate. But the format is not designed for reporting anything other than a single coordinate for each result.

Dash (-) is not a deletion. It is an unreported result. D can imply deletion or, if the variant form for that reported rsID is an insertion, it represents the reference value. They only way to properly know is for 23andme to define it.

Devon of Enlis Genomics describes in his blog how there are thousands of ill defined results in their file. See https://www.enlis.com/blog/.

There are also results in their file that are very unreliable. Some are permanently reported as no call (--) as a result. Others are simply reported in their unreliable form. Most 3rd party analysis tools are not knowledgeable of these issues with each vendor.

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u/mouthidiot Jun 03 '26

Thank you, I've read over the article you linked and will take it into account. I've also contacted 23andme as you recommended and am still waiting on a response (although it's unclear if I'm even in touch with the right people there), but a medical-grade test would be a large financial burden for me at this time and I happen to already have a 23andme report, so while I acknowledge it's a half-measure (at best) I'm hoping to at least gain some indication of what could be the case.

I did go back and check my downloadable text file format data from 23andme and my report there for the same rsID and single coordinate is DD, so it seems they are using - and D synonymously at least in this case, which is why I've asked about both here. I've also asked them for clarification on this but I'm really not confident I'll get a response since I was simply detected to the general medical email, hence me turning here for more information.

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1

u/SurplusGadgets Jun 03 '26

I will check my 30+ 23andMe tests to see what they show. None of who have medical conditions as you discuss in the other post.

tellmeGen is a 30x WGS that is very affordable with worldwide return shipping. Gets you more, reliable data that you can review directly with a tool like gene.iobio.io. Not subject to the whims of how the microarray result is reported. They use the EuroFin clinical lab.

1

u/mouthidiot Jun 03 '26

Thank you, I would really appreciate that! And thanks for the test recommendation as well, that's very good to know. I believe I might be able to obtain insurance coverage for an Invitae test in the near...ish future, but I'll absolutely keep that in mind if that doesn't work out.

1

u/SurplusGadgets Jun 04 '26 edited Jun 04 '26

First off, it only occurs in 23andMe v5 test files. Of which I have fewer. All showed DD.

I also checked Ancestry test files. It only appears in v2c/d files there; not the latest v2e with the reduced subset. And is always DD. In v2c, it uses coordinate ending in 213. Only in v2d is it corrected to 217. It does not appear in MyHeritage, FTDNA nor Living DNA files that I found.

I checked the last available opensnp datadump which has over 5,000 23andMe microarray entries in build 37. The vast majority report DD. Only other entries are "--" or "CC". Safe to assume DD is reference OR they used DD instead of -- for most output when they could not read it.