Genetic variant
rs3892097 a variant in the CYP2D6 gene
rs3892097 is a single-letter difference in the CYP2D6 gene, on chromosome 22. ClinVar, the public archive of variant interpretations, lists it as likely benign: probably harmless. It has been reported in connection with Debrisoquine, poor metabolism of and Tamoxifen response, among others. Carrying it does not, on its own, mean you have or will develop any condition.
What is this?
Your DNA is a long sequence of four letters. At a few million positions, people commonly differ by a single letter; each of those positions is called a SNP (“snip”), and rs3892097 is the catalogue number of one of them, in the CYP2D6 gene. Which letters you carry there — one copy from each parent — is your genotype.
CYP2D6 (cytochrome P450 family 2 subfamily D member 6 (gene/pseudogene)): This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and is known to metabolize as many as 25% of commonly prescribed drugs.
Gene description from NCBI Gene
The normal (or wild type) form of this SNP is a (G). The (A) form disrupts proper mRNA formation, re...
From SNPedia
Why might it matter?
ClinVar records this variant as likely benign, meaning probably harmless. A classification describes the variant, not you: what it means for one person depends on their genotype, their family history and often on other genes and circumstances.
Conditions it has been reported with
- Debrisoquine, poor metabolism of
- Tamoxifen response
- Tramadol response
- Deutetrabenazine response
- Familial cancer of breast
- Uveal melanoma
- Malignant lymphoma, large B-cell, diffuse
- Melanoma
- Uterine carcinosarcoma
- Acute myeloid leukemia
Listed in ClinVar submissions for this variant. Being listed is a report of an association, not a statement that the variant causes the condition in any given person.
Medicines
Never start, stop or change a medicine because of a genetic result without speaking to the prescriber.
Do I have this variant?
If you have taken a consumer DNA test (23andMe, AncestryDNA and similar), you can download its raw data file and check. Create a free account, upload the file, and this page will show the letters you carry at rs3892097, if your test read this position.
Connect this with your blood results
A gene is a fixed instruction; a blood test shows what your body is doing now. CheckMyBloods reads the two side by side, so a variant can be set against the markers it could plausibly affect.
Blood markers do not diagnose a genetic condition, and a variant does not explain a blood result on its own. Together, with symptoms and family history, they give a clinician context.
What should I do next?
- Find out whether you carry it. Reading about a variant says nothing about you until you know your genotype.
- Put it in context. Add your blood results, so the variant can be read against what your body is doing.
- Ask questions. Dr. Hemsworth, our AI assistant, can explain this variant and your results in plain English.
- Take anything that worries you to a professional. A GP or genetic counsellor can order a confirmatory test and interpret it with your history.
This page is general information drawn from public research databases. It cannot diagnose anything, and it is not a substitute for advice from a doctor or genetic counsellor who knows your history.
Technical details
- dbSNP ID
- rs3892097
- Gene
- CYP2D6
- Position (GRCh38)
- chr22:42128944
- Variant type
- snv
- Consequence
- splice acceptor variant
- ClinVar classification
- Likely benign; drug response; other
Genome-wide association studies (3)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| Plasma solanidine levels in chronic kidney disease | T | OR 0.82 | 5E-51 | PubMed |
| Urinary metabolite levels in chronic kidney disease | T | OR 1.7 | 6E-16 | PubMed |
| Urine alpha-hydroxymetoprolol levels in chronic kidney disease | T | OR 1.67 | 1E-15 | PubMed |
How common the less frequent letter is
- gnomAD ALL
- 100%
- 1kG AFR
- 93.9%
- 1kG ALL
- 90.7%
- 1kG AMR
- 13%
- 1kG EAS
- 0.2%
- 1kG EUR
- 18.6%
- 1kG SAS
- 10.9%
Sources
- dbSNP: rs3892097 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: CYP2D6
- Ensembl: CYP2D6
- GWAS Catalog — association studies