rs249954
A SNP in the PALB2 gene on chromosome 16. Its most notable genotype is A;A: Potentially increased risk of Breast Cancer
- Gene
- PALB2
- Location
- Chr 1623,629,146 (GRCh38)
- Highest magnitude
- 1.2Minor
- Tested on
- 23andMe, AncestryDNA
- Minor allele frequency
- 33%
Genotypes
Plus strand, as in 23andMe and AncestryDNA files.
- G;GGoodcommon in clinvar
- A;GBadPotentially increased risk of Breast Cancer
- A;AMost notableBadPotentially increased risk of Breast Cancer
SNPedia records rs249954 on the minus strand: (C;C), (C;T), (T;T). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.
Frequency
Share of each genotype in 11 HapMap populations.
- AverageG;G 42% A;G 44% A;A 14%
- European ancestry (Utah)G;G 67% A;G 30% A;A 4%
- Han Chinese (Beijing)G;G 40% A;G 44% A;A 16%
- Japanese (Tokyo)G;G 38% A;G 52% A;A 10%
- Yoruba (Nigeria)G;G 27% A;G 52% A;A 21%
- African ancestry (Southwest US)G;G 39% A;G 48% A;A 13%
- Chinese (Denver)G;G 37% A;G 50% A;A 14%
- Gujarati IndianG;G 55% A;G 35% A;A 10%
- Luhya (Kenya)G;G 28% A;G 46% A;A 26%
- Mexican ancestry (Los Angeles)G;G 54% A;G 39% A;A 7%
- Maasai (Kenya)G;G 17% A;G 49% A;A 34%
- TuscanG;G 56% A;G 41% A;A 3%
Related
Conditions, medicines and genes
Other PALB2 SNPs
- rs118203997T;TFanconi anemia, complementation group NVery important
- rs118203998C;CFanconi anemia, complementation group NVery important
- rs118203999A;AFanconi anemia, complementation group NVery important
- rs180177083A;AFanconi anemia, complementation group NVery important
- rs180177084-;-Fanconi anemia, complementation group NVery important
- rs180177085-;-Fanconi anemia, complementation group NVery important
- rs180177090-;-Fanconi anemia, complementation group NVery important
- rs180177091A;AFanconi anemia, complementation group NVery important
Notes
From SNPedia
Show notes, about 150 words
rs249954, also known as 2586+58C>T, is an intronic SNP in the PALB2 gene. There is conflicting literature about the association of this SNP with increased risk for breast cancer, but overall, it seems as if any association between rs249954 and breast cancer is likely to be either nonexistent or at least fairly small. Specifically: * ClinVar tags this SNP as benign, based on a single submission * A 2008 study of 1,000 Chinese with breast cancer reports a 36% increase in breast cancer risk (odds ratio 1.36, CI: 1.13-1.64, p = 0.001; TT/TC versus CC genotypes) * A 2010 study of 660 Chinese patients did not find an association for this SNP * A 2010 study of Polish patients reported an allele frequency of 5.7% (4 out of 70) in those patients but did not report the frequency in matched controls * A 2013 study of ~100 (male) Spanish patients reports no difference in allele frequency between patients and controls
Source and license
Adapted from rs249954 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.
SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.