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rs249954

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(C;C) 0 common in clinvar
(C;T) 1.1 slight if any increased risk of Breast Cancer
(T;T) 1.2 either no, or slightly increased risk, of Breast Cancer
ReferenceGRCh38 38.1/141
Chromosome16
Position23629146
GenePALB2
is asnp
is mentioned by
dbSNPrs249954
ebirs249954
HLIrs249954
Exacrs249954
Varsomers249954
Maprs249954
PheGenIrs249954
hapmaprs249954
1000 genomesrs249954
hgdprs249954
ensemblrs249954
gopubmedrs249954
geneviewrs249954
scholarrs249954
googlers249954
pharmgkbrs249954
gwascentralrs249954
openSNPrs249954
23andMers249954
23andMe allrs249954
SNP Nexus

SNPshotrs249954
SNPdbers249954
MSV3drs249954
GWAS Ctlgrs249954
GMAF0.3338
Max Magnitude1.2

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 20122277OA-icon.png]
  • A 2013 study of ~100 (male) Spanish patients reports no difference in allele frequency between patients and controls[PMID 23935836OA-icon.png]
? (C;C) (C;T) (T;T) 28

[PMID 19921424] Five common single nucleotide polymorphisms in the PALB2 gene and susceptibility to breast cancer in eastern Chinese population

ClinVar
Risk rs249954(T;T)
Alt rs249954(T;T)
Reference rs249954(C;C)
Significance Non-pathogenic
Disease Familial cancer of breast
Variation info
Gene PALB2
CLNDBN Familial cancer of breast
Reversed 1
HGVS NC_000016.9:g.23640467G>A
CLNSRC PALB2 database
CLNACC RCV000114539.1,



[PMID 18794107] Association of common PALB2 polymorphisms with breast cancer risk: a case-control study.

[PMID 20122277OA-icon.png] A novel germline PALB2 deletion in Polish breast and ovarian cancer patients.

GWAS snp
PMID [PMID 23453885OA-icon.png]
Trait Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)
Title Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
Risk Allele A
P-val 2E-6
Odds Ratio 1.07 [1.04-1.10]


[PMID 26981788] Role of PALB2 Polymorphisms with Regard to Susceptibility to Female Breast Cancer Risk in the Chinese Population.