rs249954

minus

Geno	Mag	Summary
(C;C)	0	common in clinvar
(C;T)	1.1	Potentially increased risk of Breast Cancer
(T;T)	1.2	Potentially increased risk of Breast Cancer

Reference

GRCh38 38.1/141

Chromosome

16

Position

23629146

Gene

PALB2

is a	snp
is	mentioned by
dbSNP	rs249954
dbSNP (classic)	rs249954
ClinGen	rs249954
ebi	rs249954
HLI	rs249954
Exac	rs249954
Gnomad	rs249954
Varsome	rs249954
LitVar	rs249954
Map	rs249954
PheGenI	rs249954
Biobank	rs249954
1000 genomes	rs249954
hgdp	rs249954
ensembl	rs249954
geneview	rs249954
scholar	rs249954
google	rs249954
pharmgkb	rs249954
gwascentral	rs249954
openSNP	rs249954
23andMe	rs249954
SNPshot	rs249954
SNPdbe	rs249954
MSV3d	rs249954
GWAS Ctlg	rs249954

GMAF

0.3338

Max Magnitude

1.2

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 20122277 ]
A 2013 study of ~100 (male) Spanish patients reports no difference in allele frequency between patients and controls[PMID 23935836 ]

?

(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 20122277 ] A novel germline PALB2 deletion in Polish breast and ovarian cancer patients.

GWAS snp
PMID	[PMID 23453885 ]
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.