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Here are my rare SNPs (click on thumbnail below). The first one is Pseudo Tay Sachs I think.
Interesting. The rsID is rs138058578, and it does create a missense mutation (HEXA R249W).Here are my rare SNPs (click on thumbnail below). The first one is Pseudo Tay Sachs I think.
Interesting. The rsID is rs138058578, and it does create a missense mutation (HEXA R249W).
You have to search without the "rs" at the frontI couldn't find that RS number in dbSNP: http://www.ncbi.nlm.nih.gov/snp/?term=rs138058578&SITE=NcbiHome&submit=Go
Well, I don't know what the old one was like, but the current one just gave me a headacheFYI: GEDmatch has a much for friendly interface now. Just looked at it and it has changed since I last used it.
You have to search without the "rs" at the front
Actually, I clicked on 23andMe's automatic linking from my result to the dbSNP site -- like I always do. Clicking on that link is what brought up the notice that it wasn't in the dbSNP database. So, roll your eyes at 23andMe!
Click on the rs number in the upper left area (next to "1.").How do I get from this page to the part of dbSNP that I am used to seeing, which shows the population percentages of the alleles?
Click on the rs number in the upper left area (next to "1.").
This one doesn't have the standard prevalence data for the minor allele at the top of the page, but they do have the data from a huge group at the bottom.
Here are my rare SNPs (click on thumbnail below). The first one is Pseudo Tay Sachs I think.
I haven't tried Ian Logan's minor allele program.
Yeah, when downloading the 1000genome prevalence data, I noticed that there's quite a few results which are inverted - that is, the "reference" allele is the less common one, and the "alternative" allele is the common one. Maybe GEDmatch is getting both the high and low prevalence alleles (less than 1% and greater than 99%), but not swapping the alleles to reflect the switch.The new hits turned out to be either not useful (at least in my case) or not actually rare, i.e., there were some frequency errors. Additionally, several of the gene names were outdated. Difficult to say whether it'd be worthwhile for other people to run. I did find out I apparently have a weird blood phenotype.
It's not up for testing yet - still doing some final tweaking. It's also a downloadable program, not the version usable on a website.Valentijn maybe my brain is just sleepy but where is the link to the program to test it out?? Thanks for all the effort should be interesting.