What F2 rs1799963 Means in Your 23andMe Raw Data
rs1799963 is the F2 prothrombin G20210A variant. When oriented to the 20210A risk allele, G/A or A/A raises venous clot risk, but most carriers never clot.
If your 23andMe raw data has a line for rs1799963, you are looking at the F2 prothrombin G20210A variant. Do not infer a clinical result from raw strand labels alone unless the report explicitly states it is oriented to F2 G20210A. Some files or strand conventions can show opposite-strand alleles, so A is not automatically the risk allele. When the file is explicitly oriented to the 20210A risk allele, G/G is the baseline genotype, G/A means one copy of the A risk allele, and A/A means two copies. If the result would change care, confirm it with a clinical lab. This variant does not cause a clot by itself. It is associated with higher prothrombin, which makes venous clots easier to form.
When you open a 23andMe raw file, search for rs1799963. You usually see one of three calls: G/G, G/A, or A/A. A raw 23andMe file normally gives the rsID and genotype, not a clinical variant name such as G20210A. If the file is oriented to the 20210A risk allele, G/A means one risk allele and A/A means two. The A is the variant to remember in that orientation. The G is the common version.
| Genotype | What it means | Direction of risk |
|---|---|---|
| G/G | Two common alleles | Baseline |
| G/A | One risk allele | Raised |
| A/A | Two risk alleles | Higher |
Scroll the table sideways for the rest →
The exact call depends on the chip and strand. Do not infer clinical risk from strand labels alone unless the report explicitly states it is oriented to F2 G20210A. When oriented to 20210A, G/A is the usual notation for the prothrombin G20210A variant.
The variant sits in the F2 gene on chromosome 11. F2 is the recipe for prothrombin, also called clotting factor II. Prothrombin is made in the liver and circulates in blood. When a blood vessel is damaged, prothrombin gets converted to thrombin, and thrombin turns fibrinogen into fibrin, the mesh that forms a clot. So F2's job is to keep enough prothrombin around for that system to work.
The F2 gene makes prothrombin, not the clot itself
A common mistake is to call this a "clotting gene" as if it switches a clot on. It does not. The G20210A change is not in the protein-coding part of F2. It is in the 3' untranslated region, after the protein instructions. This region helps regulate how much prothrombin is produced.
The variant is associated with higher plasma prothrombin. Studies report the increase as modest and study-dependent, with some estimates around 15 to 30 percent higher in carriers, but the exact figure varies. Homozygotes are rarer and tend to run higher still. That extra prothrombin shifts the balance of the clotting cascade. It does not create a clot. It changes the threshold at which a clot can form.
Think of prothrombin as raw material. More raw material means the system can make thrombin faster when it is activated. That matters more in veins where blood flow is slower. Deep vein thrombosis and pulmonary embolism are the two venous clots this variant is best known for.
One A copy is enough to shift the risk
You do not need two copies for this to matter. One A allele, written G/A in the 20210A orientation, is enough to raise the risk of a first venous thromboembolism. The increase is usually described as two to four times baseline. That sounds large. In absolute terms it is still uncommon. The general adult risk of a first venous clot is often quoted around 1 in 1,000 people per year. A carrier's annual risk is a few thousandths, not a few percent, unless other risks stack up.
Most carriers never have a clot. The variant is common in Europe, with roughly 2 to 4 percent of people of European ancestry carrying one copy. It is less common elsewhere. But risk is not just this one variant. Combined hormonal contraceptives, pregnancy, surgery, long flights, immobility, smoking, and obesity all multiply the baseline risk. So does another inherited clotting variant, factor V Leiden. If you carry both F2 G20210A and factor V Leiden, the risk is higher than either alone. That is why family history and provoking situations matter more than the raw genotype alone.
What the result does not tell you
A 23andMe raw data call is not a clinical lab test. It is a research or consumer array read. The genotype is right most of the time, but if this is the kind of result that would change a plan, ask for a confirmation test from a clinical lab. The raw file does not measure prothrombin activity or antigen levels. It does not check factor V Leiden, protein C, protein S, antithrombin, or antiphospholipid antibodies. It does not tell you whether you have had a silent clot. It does not tell you what to do about contraception, pregnancy, surgery, or travel.
F2 rs1799963 is a single variant with a known direction. That makes it easier to read, but still incomplete.
What to do after you see your genotype
If the call is G/G in the 20210A orientation, there is nothing specific to do. Your risk from this variant is baseline.
If the call is G/A or A/A in the 20210A orientation, mention it at your next medical visit if any of these apply:
- Personal or family history of blood clots
- Repeated miscarriages
- Starting estrogen-containing contraception
- Pregnancy planning
- Upcoming surgery
Write the genotype down as "F2 G20210A heterozygous" or "homozygous", not just the rsID. That is the name a clinician will recognize.
The single line worth remembering: once you confirm the 20210A risk allele, A at rs1799963 means higher prothrombin and higher venous clot risk, but most carriers never clot.
The download steps for 23andMe, on the page itself.
The short version: what is worth acting on, first.
You do not need to panic. You do need to make sure the finding is not ignored if another clotting risk appears. The free HealthOSX DNA tool, whose DNA story needs no account, supports raw files from 23andMe, AncestryDNA, MyHeritage, FamilyTreeDNA, Living DNA, WeGene, and whole-genome VCFs. For the trait and health report, the file is read in the browser and does not leave your device. Ancestry is optional and needs a server; only the needed markers are sent, and they are deleted afterwards unless you choose to keep the file. The F2 report finding is "F2 (prothrombin): The second-commonest inherited clotting variant". A VCF without rsIDs gets ancestry only; the trait and health report needs rsIDs. See the report at healthosx.com/dna.
New to raw DNA files? Start with the full guide: How to Download & Analyze Your 23andMe Raw Data Free
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HealthOS Research