Gene Knowledge Graph
UTC

Links from this page to related variants, conditions, drugs and topics are not included for automated readers. Those connections are the Gene Knowledge Graph and are licensed as data: https://www.mygenelog.com/license

Standard

Sex hormone-binding globulin levels

CHEK2 · rs6005840

Stands on its own. Nothing else here links to this position yet — but the page above is the point: what the research found, what each genotype means, and where it came from, in language you can read. Links to conditions, drugs and the senses appear automatically if we write them.

Strength of the evidence

2 / 4

Its strongest genetic-study result is p = 10−38, with 7 associations in the GWAS Catalog.

How this is scored

4: ClinVar disease-causing, reviewed by an expert panel or a guideline (3–4 stars). 3: ClinVar, several labs agreeing (2 stars), or a genetic study at p ≤ 10−50. 2: ClinVar from one lab (1 star), or p ≤ 10−20. 1: ClinVar submitted without criteria (0 stars), or genome-wide significance (p ≤ 5×10−8). The higher of the two counts. It says how solid the evidence is, not whether it matters for a particular person.

What the study found

Who was studied 180,726 European ancestry men.

The effect Each copy of the A allele shifted the measure 0.0169 higher (95% confidence interval 0.014-0.019); p = 4 × 10−39.

How common The A allele had a frequency of about 33% in the people studied.

Where it sits Chromosome 22, band 22q12.1 — in an intron of CHEK2.

How common each version is

AG
Korean KRGDB
G 100.0%
Korean Korea4K
A 17.3% · G 82.7%
Korean Korea1K
A 17.4% · G 82.6%
Japanese ToMMo
A 11.3% · G 88.7%
Vietnamese
A 12.4% · G 87.6%
World gnomAD
A 32.6% · G 67.4%
World 1000 Genomes
A 28.5% · G 71.5%
World TOPMed
A 33.7% · G 66.3%

By ancestry gnomAD

East Asian
A 16.0% · G 84.0%
European (non-Finnish)
A 30.4% · G 69.6%
African / African American
A 41.5% · G 58.5%
South Asian
A 16.9% · G 83.1%
Admixed American (Latino)
A 36.0% · G 64.0%
Middle Eastern
A 23.6% · G 76.4%
Finnish
A 26.5% · G 73.5%
Ashkenazi Jewish
A 21.7% · G 78.3%

The share of all copies of this position that are each version. Source: the population studies published in dbSNP (US NCBI); each row names its study. The ancestry rows are gnomAD's own groups (via Ensembl), as the survey defines them, not races.

What each result means

A/A Two copies of the version the research linked to Sex hormone-binding globulin levels. That is the strongest link of the three results. A link in a study is not a diagnosis.
A/G One copy of the version the research linked to Sex hormone-binding globulin levels. That is a smaller link than two copies.
G/G No copy of the version the research linked to Sex hormone-binding globulin levels. This is the starting point the study compared everyone against.
Source
Using human genetics to understand the disease impacts of testosterone in men and women
Ruth KS, Day FR, Tyrrell J, Thompson DJ, Wood AR, Mahajan A, Beaumont RN, Wittemans L, Martin S, Busch AS, Erzurumluoglu AM, Hollis B
and 10 more — show all
O'Mara TA, McCarthy MI, Langenberg C, Easton DF, Wareham NJ, Burgess S, Murray A, Ong KK, Frayling TM, Perry JRB
Endometrial Cancer Association Consortium
Nature medicine · 2020 · PMID 32042192 · open access

Quoting this page

Licensed CC BY-NC 4.0: free to read, share and adapt for non-commercial use, naming MyGeneLog™ and linking the exact page. Commercial use, including training or serving a commercial AI system, needs a licence — https://www.mygenelog.com/license

Sex hormone-binding globulin levels (rs6005840). MyGeneLog™. https://www.mygenelog.com/variants/rs6005840

← See all variants