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dbSNP Short Genetic Variations

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs10771399

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:28002147 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.09566 (12012/125568, TOPMED)
G=0.0904 (2831/31326, GnomAD)
G=0.103 (515/5008, 1000G) (+ 5 more)
G=0.089 (397/4480, Estonian)
G=0.122 (472/3854, ALSPAC)
G=0.113 (419/3708, TWINSUK)
G=0.12 (72/600, NorthernSweden)
G=0.15 (32/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
15 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 12 NC_000012.12:g.28002147A>G
GRCh37.p13 chr 12 NC_000012.11:g.28155080A>G
GRCh38.p12 chr 12 alt locus HSCHR12_1_CTG2 NW_003315938.1:g.114691T>C
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.90434 G=0.09566
gnomAD - Genomes Global Study-wide 31326 A=0.9096 G=0.0904
gnomAD - Genomes European Sub 18848 A=0.8957 G=0.1043
gnomAD - Genomes African Sub 8704 A=0.962 G=0.038
gnomAD - Genomes East Asian Sub 1552 A=0.780 G=0.220
gnomAD - Genomes Other Sub 1086 A=0.911 G=0.089
gnomAD - Genomes American Sub 846 A=0.92 G=0.08
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.90 G=0.10
1000Genomes Global Study-wide 5008 A=0.897 G=0.103
1000Genomes African Sub 1322 A=0.966 G=0.034
1000Genomes East Asian Sub 1008 A=0.823 G=0.177
1000Genomes Europe Sub 1006 A=0.894 G=0.106
1000Genomes South Asian Sub 978 A=0.86 G=0.14
1000Genomes American Sub 694 A=0.93 G=0.07
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.911 G=0.089
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.878 G=0.122
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.887 G=0.113
Northern Sweden ACPOP Study-wide 600 A=0.88 G=0.12
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.85 G=0.15
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement A= G Note
GRCh38.p12 chr 12 NC_000012.12:g.28002147= NC_000012.12:g.28002147A>G
GRCh37.p13 chr 12 NC_000012.11:g.28155080= NC_000012.11:g.28155080A>G
GRCh38.p12 chr 12 alt locus HSCHR12_1_CTG2 NW_003315938.1:g.114691= NW_003315938.1:g.114691T>C
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

48 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16001756 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss16570941 Feb 27, 2004 (120)
3 SC_SNP ss18513257 Feb 27, 2004 (120)
4 SC_SNP ss18968891 Feb 27, 2004 (120)
5 SSAHASNP ss20872600 Apr 05, 2004 (121)
6 ABI ss38914988 Mar 13, 2006 (126)
7 ENSEMBL ss161513565 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss170640813 Jul 04, 2010 (132)
9 1000GENOMES ss225670570 Jul 14, 2010 (132)
10 1000GENOMES ss235874703 Jul 15, 2010 (132)
11 1000GENOMES ss242442777 Jul 15, 2010 (132)
12 GMI ss281324242 May 04, 2012 (137)
13 PJP ss291408243 May 09, 2011 (134)
14 TISHKOFF ss563070225 Apr 25, 2013 (138)
15 SSMP ss658609967 Apr 25, 2013 (138)
16 EVA-GONL ss989368284 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1078344323 Aug 21, 2014 (142)
18 1000GENOMES ss1344393792 Aug 21, 2014 (142)
19 HAMMER_LAB ss1397630252 Sep 08, 2015 (146)
20 DDI ss1426883226 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1576185951 Apr 01, 2015 (144)
22 EVA_DECODE ss1599042685 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1628270175 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1671264208 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1932731028 Feb 12, 2016 (147)
26 GENOMED ss1967555318 Jul 19, 2016 (147)
27 JJLAB ss2027115132 Sep 14, 2016 (149)
28 CLINVAR ss2136309354 Nov 14, 2016 (149)
29 USC_VALOUEV ss2155441712 Dec 20, 2016 (150)
30 TOPMED ss2352434522 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2628037893 Nov 08, 2017 (151)
32 ILLUMINA ss2635035252 Nov 08, 2017 (151)
33 GRF ss2699771948 Nov 08, 2017 (151)
34 ILLUMINA ss2710757495 Nov 08, 2017 (151)
35 GNOMAD ss2908710933 Nov 08, 2017 (151)
36 AFFY ss2985613724 Nov 08, 2017 (151)
37 SWEGEN ss3009409090 Nov 08, 2017 (151)
38 ILLUMINA ss3021417782 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3027365243 Nov 08, 2017 (151)
40 TOPMED ss3166107643 Nov 08, 2017 (151)
41 CSHL ss3349985541 Nov 08, 2017 (151)
42 ILLUMINA ss3651792270 Oct 12, 2018 (152)
43 EGCUT_WGS ss3676725688 Jul 13, 2019 (153)
44 EVA_DECODE ss3693355524 Jul 13, 2019 (153)
45 ILLUMINA ss3725313672 Jul 13, 2019 (153)
46 ACPOP ss3738880715 Jul 13, 2019 (153)
47 EVA ss3750288906 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3815608959 Jul 13, 2019 (153)
49 1000Genomes NC_000012.11 - 28155080 Oct 12, 2018 (152)
50 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 28155080 Oct 12, 2018 (152)
51 Genetic variation in the Estonian population NC_000012.11 - 28155080 Oct 12, 2018 (152)
52 gnomAD - Genomes NC_000012.11 - 28155080 Jul 13, 2019 (153)
53 Northern Sweden NC_000012.11 - 28155080 Jul 13, 2019 (153)
54 TopMed NC_000012.12 - 28002147 Oct 12, 2018 (152)
55 UK 10K study - Twins NC_000012.11 - 28155080 Oct 12, 2018 (152)
56 A Vietnamese Genetic Variation Database NC_000012.11 - 28155080 Jul 13, 2019 (153)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss170640813, ss281324242, ss291408243, ss1397630252, ss1599042685, ss2635035252 NC_000012.10:28046346:A:G NC_000012.12:28002146:A:G (self)
57120146, 31721925, 22463936, 155914886, 12165580, 31721925, 7039189, ss225670570, ss235874703, ss242442777, ss563070225, ss658609967, ss989368284, ss1078344323, ss1344393792, ss1426883226, ss1576185951, ss1628270175, ss1671264208, ss1932731028, ss1967555318, ss2027115132, ss2155441712, ss2352434522, ss2628037893, ss2699771948, ss2710757495, ss2908710933, ss2985613724, ss3009409090, ss3021417782, ss3349985541, ss3651792270, ss3676725688, ss3738880715, ss3750288906 NC_000012.11:28155079:A:G NC_000012.12:28002146:A:G (self)
80462130, ss2136309354, ss3027365243, ss3166107643, ss3693355524, ss3725313672, ss3815608959 NC_000012.12:28002146:A:G NC_000012.12:28002146:A:G (self)
ss16001756, ss16570941, ss18513257, ss18968891, ss20872600 NT_009714.16:20914053:A:G NC_000012.12:28002146:A:G (self)
ss38914988, ss161513565 NT_009714.17:20915203:A:G NC_000012.12:28002146:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

15 citations for rs10771399
PMID Title Author Year Journal
22267197 Genome-wide association analysis identifies three new breast cancer susceptibility loci. Ghoussaini M et al. 2012 Nature genetics
22348646 Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. Antoniou AC et al. 2012 Breast cancer research
22747683 Genetic variants associated with breast size also influence breast cancer risk. Eriksson N et al. 2012 BMC medical genetics
23535825 Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls. Zheng W et al. 2013 Human molecular genetics
23544014 Evidence of gene-environment interactions between common breast cancer susceptibility loci and established environmental risk factors. Nickels S et al. 2013 PLoS genetics
24025454 Hereditary breast cancer: ever more pieces to the polygenic puzzle. Bogdanova N et al. 2013 Hereditary cancer in clinical practice
24771903 Breast Cancer Risk - From Genetics to Molecular Understanding of Pathogenesis. Fasching PA et al. 2013 Geburtshilfe und Frauenheilkunde
24941967 Breast cancer risk assessment using genetic variants and risk factors in a Singapore Chinese population. Lee CP et al. 2014 Breast cancer research
25476496 A genetic variant at 12p11 significantly modifies breast cancer risk in a genetically homogenous island population. McVeigh TP et al. 2015 Breast cancer research and treatment
26510858 Patients with a High Polygenic Risk of Breast Cancer do not have An Increased Risk of Radiotherapy Toxicity. Dorling L et al. 2016 Clinical cancer research
26884359 Genetic predisposition to ductal carcinoma in situ of the breast. Petridis C et al. 2016 Breast cancer research
27117709 Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer. Couch FJ et al. 2016 Nature communications
27392074 The Relationship between Common Genetic Markers of Breast Cancer Risk and Chemotherapy-Induced Toxicity: A Case-Control Study. Dorling L et al. 2016 PloS one
27424552 Genomics era and complex disorders: Implications of GWAS with special reference to coronary artery disease, type 2 diabetes mellitus, and cancers. Pranavchand R et al. 2016 Journal of postgraduate medicine
27459855 Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus. Zeng C et al. 2016 Breast cancer research

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post246+3cda961