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)[PMID 1879410]
- A 2010 study of 660 Chinese patients did not find an association for this SNP [PMID 19921424]
- 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 [PMID 20122277]
- A 2013 study of ~100 (male) Spanish patients reports no difference in allele frequency between patients and controls[PMID 23935836]
[PMID 20122277] A novel germline PALB2 deletion in Polish breast and ovarian cancer patients.