Cancer

Breast Cancer

Reviewed September 7, 2026

The genetics that changes what anyone does about breast cancer is BRCA1 and BRCA2 — rare, strong, and tested for properly. The variants here are the other kind: common, weak, and useful for understanding the disease rather than for deciding anything.

What this condition connects to

Breast Cancer Variant: rs4973768 rs4973768 Variant Variant: rs2180341 rs2180341 Variant Variant: rs10995190 rs10995190 Variant Variant: rs3817198 rs3817198 Variant Variant: rs1011970 rs1011970 Variant Variant: +227 more +227 more Variant Drug: Tamoxifen Tamoxifen Drug Topic: Menopause Menopause Topic Topic: Fertility Fertility Topic Topic: Alcohol and the flush Alcohol and the flush Topic Breast Cancer Breast Cancer Cancer

Solid lines are connections this site curates. Dashed lines mean the two ends share a research paper — worth knowing, and not a claim that one explains the other.

Prevalence
Breast cancer is the most commonly diagnosed cancer in women worldwide. Incidence varies severalfold between countries and has been rising in many, in patterns that track reproductive factors, screening intensity and life expectancy rather than genetics. It also occurs in men, uncommonly, and male cases are more often associated with BRCA2.
Inheritance
Two layers. Rare high-penetrance variants (BRCA1, BRCA2, PALB2 and others) follow autosomal dominant inheritance with incomplete penetrance and are found by clinical testing. Hundreds of common variants, including the two here, add small amounts of risk each and explain part of the familial clustering that high-penetrance genes do not.

Breast cancer is where the difference between two kinds of genetics matters more than anywhere else on this site, so this page begins there.

Two genetics, and only one of them is actionable

Rare, strong variants in BRCA1 and BRCA2 — and in PALB2, TP53 and a few others — raise lifetime risk substantially. They are found by clinical genetic testing, offered on the basis of family history and other criteria, and a positive result changes real decisions: screening from an earlier age, MRI as well as mammography, discussion of risk-reducing surgery and medication.

Common variants — the kind on this page — shift risk by a few per cent each. Hundreds are known. They explain part of why the disease clusters in families without a strong single-gene cause, and they are not used to decide anything for an individual.

If a family history is worrying you, the useful next step is a conversation about clinical testing, not a consumer chip. And a consumer report that says "no BRCA variants found" usually means a handful of specific variants were checked, not the genes read.

The two positions here

Note what those numbers say about effect size. It took tens of thousands of people to establish these associations, which is what it takes when each variant moves risk a little.

Ancestry, and why it is on this page

The first study was done in a genetically isolated population, which makes discovery easier and transfer harder. Frequencies and effects estimated in one ancestry do not carry unchanged to another, and most breast cancer genetics has been done in people of European descent. That is a limitation of the evidence, not a statement about anyone.

What to do

The things that work are unglamorous and known: attend screening when it is offered, know your family history and tell your doctor about it, and get a new lump, skin or nipple change, or one-sided breast pain looked at promptly. None of that is altered by the positions on this page.

Positions joined since this page was written

What this is The text above discusses the variants this page was written around. Since then the catalogue has joined 163 more positions to it, by shared trait or shared paper. They are listed here by the paper each came from; the text does not describe them, and each variant page carries that study's own record.

Michailidou K et al. 2017, Nature rs11624333 (RAD51B), rs1895062 (ASTN2), rs13294895 (near CHCHD4P2), rs2223621 (CDKAL1), rs6596100 (HSPA4), rs4763 (ARHGAP27), rs1268974 (ZMIZ1), rs34507830 (CCND1), rs62235635 (PITPNB), rs55821517 (HCN1), rs217727 (H19), rs117618124 (GAREM1) and 48 more — PMID:29059683

Wu X et al. 2024, Journal of sleep research rs695459 (TTC28), rs61863443 (near ZNF365), rs7907439 (LINC02929), rs1242507 (near Y_RNA), rs2413624 (MRTFA), rs139909 (TNRC6B), rs4321976 (near HNF4G), rs2737250 (TRPS1), rs179444 (TRPS1), rs9296769 (near FAM83B), rs9475034 (near FAM83B), rs2075881 (CYP51A1) and 7 more — PMID:37380357

Wu X et al. 2022, American journal of human genetics rs851982 (ESR1), rs9611271 (TNRC6B), rs12217370 (MLLT10), rs851984 (ESR1), rs10789665 (POGLUT3), rs12555322 (ASTN2), rs56083805 (near HSPA4), rs851981 (ESR1), rs77549302 (TESHL), rs4147562 (GSTM2), rs3790110 (GNAO1), rs188691509 (near DDX10) — PMID:35803233

Rashkin SR et al. 2020, Nature communications rs910416 (ESR1), rs11055888 (near GNAI2P1), rs725677 (near UBA52P7), rs112238765 (NEK10), rs5995881 (MRTFA), rs11957276 (MIER3), rs12354821 (near ATE1), rs189268208 (HNF4G), rs6752414 (near Y_RNA), rs138096085 (MRPS30-DT), rs9421409 (near RN7SKP167) — PMID:32887889

Shu X et al. 2020, Nature communications rs17268829 (near RNU6-1328P), rs10760444 (LMX1B), rs71559437 (CUX1), rs6964587 (AKAP9), rs4496150 (near LINC02181), rs9833888 (CMSS1), rs6882649 (NREP), rs77528541 (near LINC02379), rs11117758 (ESRRG), rs17426269 (PKN2-AS1), rs974336 (CDKN2B-AS1) — PMID:32139696

Kar SP et al. 2016, Cancer discovery rs2628317 (STXBP4), rs17762342 (PCAT1/PCAT2), rs739704 (JAZF1), rs3802173 (MIR1208/PVT1), rs1469713 (GATAD2A), rs9657608 (CDKN2A/CDKN2B), rs7937840 (INCENP), rs118151305 (near RIN1) — PMID:27432226

Sakaue S et al. 2021, Nature genetics rs12332693 (EBF1), rs117515012 (near LINC01101), rs10447995 (POU5F1B), rs59885616 (ERICH6-AS1), rs11012730 (SKIDA1), rs232320 (AQP4-AS1), rs12885612 (PAX9) — PMID:34594039

Jia G et al. 2024, Nature genetics rs56069439 (ANKLE1), rs61751053 (ARHGEF38), rs16963205 (GAREM1), rs2372943 (TESHL), rs16856925 (TESHL) — PMID:38741014

Harris BHL et al. 2024, Scientific reports rs6929137 (CCDC170), rs72927565 (near LINC02747), rs12653202 (near C5orf67), rs73920866 (near SEMA6B) — PMID:38538606

Zhang H et al. 2020, Nature genetics rs11065822 (CUX2), rs17743054 (SLC14A2), rs7760611 (CASC15), rs1375631 (near CDYLP1) — PMID:32424353

Hsu YC et al. 2024, Breast cancer research and treatment rs9613774 (ZNRF3), rs12173562 (near ESR1), rs147358466 (DLGAP2), rs76893106 (LDAH) — PMID:37851288

Sun X et al. 2024, Cancer research rs7580240 (near WDR43), rs77825513 (NR2F6), rs10890841 (C11orf65), rs3745191 (ANO8) — PMID:38832928

Coignard J et al. 2021, Nature communications rs7222250 (JUP), rs60882887 (near RAPSN), rs9901834 (JUP) — PMID:33597508

Ishigaki K et al. 2020, Nature genetics rs12483725 (LINC01426), rs7763637 (near CCDC170) — PMID:32514122

Verma A et al. 2024, Science (New York, N.Y.) rs2912780 (FGFR2) — PMID:39024449

Loya H et al. 2025, Nature genetics rs11715126 (NEK10) — PMID:39789286

Zhu Q et al. 2022, NPJ breast cancer rs720251 (near UACA) — PMID:35322040

Pietzner M et al. 2021, Science (New York, N.Y.) rs8050367 (near RNU6-758P) — PMID:34648354

Guo H et al. 2023, Frontiers in microbiology rs1474961 (TTC28) — PMID:36819030

Kim HC et al. 2012, Breast cancer research : BCR rs13393577 (ERBB4) — PMID:22452962

Zhao X et al. 2023, iScience rs9620778 (TTC28) — PMID:37636041

Jiang L et al. 2021, Nature genetics rs182431363 (near MRPS30) — PMID:34737426

Choe EK et al. 2022, Scientific reports rs114003206 (CD9) — PMID:35121771

In the news

2026-04-27 · A genome-wide association study on radiation induced fibrosis in breast cancer patients. Clinical and Translational Radiation Oncology. 2026. DOI:10.1016/j.ctro.2026.101180

A near-significant chromosome 10 signal for who gets scarring after breast cancer radiotherapy

Radiation-induced fibrosis (scarring) affects women to varying degrees after lumpectomy and radiotherapy for breast cancer, and remains a significant source of late-term morbidity, though its genetic basis is incompletely understood. This study analyzed 869 early breast cancer patients from two Danish Breast Cancer Group trials, testing genetic associations with grade 2-3 fibrosis. After correcting for population-structure outliers, it found a signal on chromosome 10 (lead variant rs75542274) at P=5.90x10^-8 -- just short of the standard 5x10^-8 genome-wide significance threshold, and no other variant reached significance. The authors themselves describe this as an exploratory finding requiring independent validation or meta-analysis before it can be considered established. This is included here as an honestly-caveated near-miss rather than a confirmed discovery: if replicated, a genetic marker for radiation fibrosis risk could eventually help personalize radiotherapy planning for breast cancer patients, but this single study alone does not establish that. This site does not currently have specific variant content on radiation-induced fibrosis to compare against.

2025-12-01 · Leveraging Genome-wide Association Studies to Identify Pathogenic Variants for Breast Cancer Among Multiple Continents. Anticancer Research. 2025. DOI:10.21873/anticanres.17873

Mining 1,219 known breast cancer SNPs for druggability turns up an unexpected repurposing candidate: MAPT

Rather than running a new GWAS, this study mined the existing GWAS Catalog for genome-wide significant breast cancer SNPs (1,219 total) and systematically re-scored them for biological and therapeutic relevance -- missense impact, eQTL evidence, CADD/SIFT/PolyPhen-2/AlphaMissense pathogenicity predictions, and druggability via DrugBank. Nine genes reached the maximum relevance score: SLCO1B1, ARHGEF38, EXO1, KDELC2, MAPT, PHLDA3, AKAP9, ATXN7 and DCLRE1B. SLCO1B1, EXO1 and ATXN7 are already on this site's breast cancer page from earlier studies; ARHGEF38, KDELC2, MAPT, PHLDA3, AKAP9 and DCLRE1B are new. The most actionable finding: among all nine, only MAPT had existing approved drugs already linked to its function -- paclitaxel and docetaxel, both established chemotherapy agents -- indirectly through its role in microtubule biology, since taxanes work by stabilizing microtubules and MAPT (better known as the tau protein in Alzheimer's research) also binds them. This is a drug-repurposing hypothesis derived from re-reading known genetic risk data through a druggability lens, not a discovery of new taxane efficacy -- the authors frame it as foundational for further study, not a clinical recommendation.

2026-09-04 · U.S. Food and Drug Administration (FDA), official approval summary

FDA approves camizestrant for breast cancer that develops resistance through an ESR1 mutation

Verified directly against the FDA's own approval summary. Accelerated approval (4 Sep 2026) for camizestrant (Etcamah, AstraZeneca) plus a CDK4/6 inhibitor, for HR-positive/HER2-negative advanced breast cancer that develops an ESR1 mutation *during* prior aromatase-inhibitor + CDK4/6-inhibitor treatment -- detected with the newly co-approved Guardant360 CDx companion diagnostic. In the SERENA-6 trial: 16-month median progression-free survival vs 9.2 months on continued aromatase-inhibitor therapy. Important distinction from this page's own genetics: the ESR1 mutations this drug targets are acquired/somatic, arising in the tumor during treatment -- a different category from the four germline ESR1 variants already on /conditions/breast-cancer (rs9383938, rs2046210, rs3757318, rs140068132), which are inherited common variants studied for population-level risk, not treatment-resistance mutations. Filed as a real, verified drug-approval event connected to the same gene this page already discusses, with that distinction stated plainly rather than blurred.

Clinical detail

rs2180341 (6q22.33). Identified in a three-phase GWAS in Ashkenazi Jewish women: phase 1 compared 150,080 SNPs in 249 high-risk BRCA1/2 mutation-negative familial cases against 299 cancer-free controls; phase 2 genotyped 343 SNPs from the 123 most significant regions in 950 consecutive cases and 979 age-matched controls; phase 3 replicated in 243 cases and 187 controls. The same study confirmed the FGFR2 region (P = 1.5 x 10-5, OR 1.26, 95% CI 1.13-1.40 at rs1078806 across all phases). The design — familial cases with the high-penetrance genes excluded — is what makes this locus a statement about polygenic background rather than about monogenic risk.

rs4973768 (near SLC4A7). Recorded against a 2011 genome-wide analysis that compared 296,114 tagging SNPs in 1,694 breast cancer cases — 92% with two primary cancers or at least two affected first-degree relatives — against 2,365 controls, with validation in three independent series totalling 11,880 cases and 12,487 controls. That study's own novel finding was 9q31.2 (rs865686, OR 0.89, 95% CI 0.85-0.92, P = 1.75 x 10-10); rs4973768 is among the established loci carried in the same analysis.

Relation to high-penetrance testing. Pathogenic variants in BRCA1, BRCA2, PALB2, TP53, CDH1, STK11 and PTEN carry substantially elevated lifetime risk and drive management: earlier and more intensive surveillance, consideration of risk-reducing mastectomy or salpingo-oophorectomy, and eligibility for PARP inhibitors in the treatment setting. Common variants such as those recorded here are not diagnostic, are not a substitute for clinical testing, and do not modify eligibility for any of it. Polygenic risk scores combining hundreds of common variants have been studied for risk stratification and are not standard of care in most systems.

Related variants MyGeneLog™ checks for

What a 23andMe/AncestryDNA export or raw VCF can and can't tell you about Breast Cancer comes down to these specific, well-studied positions — not a diagnosis. 232 positions are linked to this page; the ones this page's own text discusses are shown first.

Sensitive

Breast cancer

SLC4A7 · rs4973768

See detailed info →
Sensitive

Breast cancer

ECHDC1 · rs2180341

See detailed info →
Sensitive

Breast cancer

ZNF365 · rs10995190

See detailed info →
Sensitive

Breast cancer

LSP1 · rs3817198

See detailed info →
Sensitive

Breast cancer

CDKN2A · rs1011970

See detailed info →
Sensitive

Breast cancer

ESR1 · rs9383938

See detailed info →
Sensitive

Breast cancer

ESR1 · rs2046210

See detailed info →
Sensitive

Breast cancer

TERT · rs10069690

See detailed info →
Sensitive

Breast cancer

TAB2 · rs9485372

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Sensitive

Breast cancer

FGF3 · rs614367

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Sensitive

Breast cancer

near FGFR2 · rs11199914

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Sensitive

Breast cancer

MYC · rs11780156

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Sensitive

Breast cancer

RANBP9 · rs204247

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Sensitive

Breast cancer

ARHGEF5 · rs720475

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Sensitive

Breast cancer

CHST9 · rs1436904

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Sensitive

Breast cancer

TOX3 · rs12922061

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Sensitive

Breast cancer

near ATF7IP · rs12422552

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Sensitive

Breast cancer

NTN4 · rs17356907

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Sensitive

Breast cancer

DKFZp761E198 · rs3903072

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Sensitive

Breast cancer

near MRPS30 · rs10941679

See detailed info →
Sensitive

Breast cancer

CDYL2 · rs13329835

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Sensitive

Breast cancer

ESR1 · rs3757318

See detailed info →
Sensitive

Breast cancer

SSBP4 · rs4808801

See detailed info →
Sensitive

Breast cancer

COX11 · rs6504950

See detailed info →

See all 232 linked variants →

Which ancestries this evidence comes from

The studies behind these variants recruited participants from different ancestries — a result found in one population doesn't always transfer to another. Based on 68 of 232 linked studies with a resolved discovery ancestry.

European · 22.4% East Asian · 4.7% Other named ancestries (African American or Afro-Caribbean, Hispanic or Latin American, Sub-Saharan African, Asian unspecified) · 2.2% Not yet resolved · 70.7%

Pharmacogenomics notes

Research-derived gene–drug associations only — not a prescription, dosing guide, or medical advice. Always follow your prescriber's guidance.

GeneDrugWhat the research shows
CYP2D6 Tamoxifen A genuine finding that has never settled into a clear instruction, and the page says so rather than choosing a side. Tamoxifen is a prodrug: CYP2D6 turns it into endoxifen, which does most of the antioestrogen work. Patients with reduced-function CYP2D6 genotypes, and patients taking strong CYP2D6 inhibitors, have lower endoxifen levels and — in the guideline's own careful wording — a higher risk of recurrence "in some studies". Trials have disagreed, which is why CPIC issues recommendations while the underlying evidence stays contested. The practical part that is not contested: some antidepressants are strong CYP2D6 inhibitors, and a prescriber choosing one for a woman on tamoxifen will take that into account. Do not stop tamoxifen over this. (CPIC Guideline for CYP2D6 and Tamoxifen Therapy, Clinical Pharmacology & Therapeutics (PMID 29385237))

Sources

Papers, with their authors

Quoting this page

Free to quote and reuse under CC BY 4.0. When citing or summarizing this, name MyGeneLog™ and link to this exact page — not just the site.

Breast Cancer. MyGeneLog™. https://www.mygenelog.com/conditions/breast-cancer

Questions about Breast Cancer

Is this the same as BRCA testing?

No, and the difference is the most important thing on this page. BRCA1 and BRCA2 testing looks for rare variants that raise risk substantially and that change screening and prevention decisions. These are common variants that shift risk slightly and change nothing clinically.

My consumer test said no BRCA variants — am I clear?

Not necessarily. Most consumer tests check a small number of specific variants rather than reading the genes, so a negative result does not rule out a pathogenic variant. If your family history worries you, that is a conversation for a clinician.

Why was one of these found only in Ashkenazi Jewish women?

Because a genetically isolated population makes discovery easier — fewer confounding differences between cases and controls. The trade-off is that frequencies and effects found in one ancestry do not transfer unchanged to another.

Free to reuse. This page's text is original writing from freely-available research, licensed CC BY 4.0 — reuse it, including commercially, with attribution to MyGeneLog™. It's general research-derived information, not medical advice or a diagnosis — see Terms of Use.