Using 23andMe/Ancestry/Family Tree DNA to identify risk allele for respiratory failure with COVID-19

Several people have asked about the risk haplotype in the post below. If you have been genotyped on Ancestry, 23andMe, and Family Tree DNA (unless you are on 23andMe after summer of 2017) there is one SNP in high LD with the causal variant you can look up. It’s rs10490770. The risk allele is C and non-risk allele T. If you download the raw data from any of these services you can find rs10490770 with a search, and look for your genotype (if by some chance it is a reverse strand, the risk allele may actually be G and the non-risk allele A).

What does risk vs. non-risk mean? You can read the original paper, Genomewide Association Study of Severe Covid-19 with Respiratory Failure. They say: “We identified a 3p21.31 gene cluster as a genetic susceptibility locus in patients with Covid-19 with respiratory failure and confirmed a potential involvement of the ABO blood-group system…”

It looks like in their sample CT = 1.75 times greater chance of severe respiratory problems, and CC = 3 times greater chance. The frequency is ~10% or less in Western Europeans, so very few people are CC (~1%). But in South Asians the risk allele is 30-40%, which means that 10-15% of people have the CC genotype!

Here are the results. Focus on rs11385942 at locus 3p21.31 (the top one):

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6 thoughts on “Using 23andMe/Ancestry/Family Tree DNA to identify risk allele for respiratory failure with COVID-19

  1. I guess the damn FDA prevented them from sharing this information after summer 2017? Ours were done in September 2017. No results for rs10490770. :/

  2. Just searched my 23andMe data and rs10490770 is not there. Did you check all the other rs positions, or is that something I should do?

  3. I downloaded my genome from 23andme after waiting 5 minutes for it to be assembled, unzipped the downloaded file and loaded it in an editor. A search quickly found rs10490770, my allele is TT.

    BTW, years ago 23andme informed me I was customer ~70,500 or so, therefore, older results are valid.

  4. I think you should mention that since this study was done on a European population the results may not hold for other populations. I don’t think south east asian countries have had a higher case fatality rate than europeans, at least to my knowledge. Italy where some of this data was generated actually had a higher fatality rate. Blacks die at a higher rate but people of African decent tend to have less Neanderthal DNA (I know black Americans are admixed, but still this should hold true at a population level.).

    I wonder if this only works for older 23andMe customers, it worked for me (I had figured this out myself looking at the papers and was going to blog about it but went to see if anyone else had already and found your blog and was lazy so just shared that instead). Anyhow, it is good resource for people.

    If you have 23andMe and are logged in, this link should take you straight to your genotype, at least if you’re on the older V3 chip like me. https://you.23andme.com/tools/data/?query=rs10490770&filter_by_platforms=true

  5. in summer of 2017 23andme switched to a new chip. that chip doesn’t have that marker (the older chips are omniexpress base and have it like ancestry and 23andme)

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