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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.

rs28897743

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr13:32346896 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00000 (1/242302, GnomAD)
A=0.00002 (2/125568, TOPMED)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRCA2 : Missense Variant
Publications
18 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 13 NC_000013.11:g.32346896G>A
GRCh38.p12 chr 13 NC_000013.11:g.32346896G>C
GRCh38.p12 chr 13 NC_000013.11:g.32346896G>T
GRCh37.p13 chr 13 NC_000013.10:g.32921033G>A
GRCh37.p13 chr 13 NC_000013.10:g.32921033G>C
GRCh37.p13 chr 13 NC_000013.10:g.32921033G>T
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.36417G>A
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.36417G>C
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.36417G>T
Gene: BRCA2, BRCA2, DNA repair associated (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA2 transcript NM_000059.3:c.7007G>A R [CGC] > H [CAC] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Arg2336His R (Arg) > H (His) Missense Variant
BRCA2 transcript NM_000059.3:c.7007G>C R [CGC] > P [CCC] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Arg2336Pro R (Arg) > P (Pro) Missense Variant
BRCA2 transcript NM_000059.3:c.7007G>T R [CGC] > L [CTC] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Arg2336Leu R (Arg) > L (Leu) Missense Variant
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.

Allele: A (allele ID: 46633 )
ClinVar Accession Disease Names Clinical Significance
RCV000009923.6 Fanconi anemia, complementation group D1 Pathogenic
RCV000031659.9 Breast-ovarian cancer, familial 2 Pathogenic
RCV000045112.9 Hereditary breast and ovarian cancer syndrome Pathogenic
RCV000131031.5 Hereditary cancer-predisposing syndrome Pathogenic
RCV000174440.5 not provided Pathogenic
RCV000475925.1 Familial cancer of breast Pathogenic
Allele: C (allele ID: 66909 )
ClinVar Accession Disease Names Clinical Significance
RCV000045113.6 Hereditary breast and ovarian cancer syndrome Pathogenic
RCV000077394.3 Breast-ovarian cancer, familial 2 Pathogenic
RCV000214499.3 Hereditary cancer-predisposing syndrome Pathogenic
RCV000256059.2 not provided Pathogenic
RCV000475905.1 Familial cancer of breast Pathogenic
Allele: T (allele ID: 66910 )
ClinVar Accession Disease Names Clinical Significance
RCV000045114.4 Hereditary breast and ovarian cancer syndrome Likely-Pathogenic
RCV000113685.1 Breast-ovarian cancer, familial 2 Pathogenic
RCV000219635.2 Hereditary cancer-predisposing syndrome Likely-Pathogenic
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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.99998 A=0.00002
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 G= A C T Note
GRCh38.p12 chr 13 NC_000013.11:...

NC_000013.11:g.32346896G=

NC_000013.11:...

NC_000013.11:g.32346896G>A

NC_000013.11:...

NC_000013.11:g.32346896G>C

NC_000013.11:...

NC_000013.11:g.32346896G>T

GRCh37.p13 chr 13 NC_000013.10:...

NC_000013.10:g.32921033G=

NC_000013.10:...

NC_000013.10:g.32921033G>A

NC_000013.10:...

NC_000013.10:g.32921033G>C

NC_000013.10:...

NC_000013.10:g.32921033G>T

BRCA2 RefSeqGene (LRG_293) NG_012772.3:g...

NG_012772.3:g.36417G=

NG_012772.3:g...

NG_012772.3:g.36417G>A

NG_012772.3:g...

NG_012772.3:g.36417G>C

NG_012772.3:g...

NG_012772.3:g.36417G>T

BRCA2 transcript NM_000059.3:c...

NM_000059.3:c.7007G=

NM_000059.3:c...

NM_000059.3:c.7007G>A

NM_000059.3:c...

NM_000059.3:c.7007G>C

NM_000059.3:c...

NM_000059.3:c.7007G>T

breast cancer type 2 susceptibility protein NP_000050.2:p...

NP_000050.2:p.Arg2336=

NP_000050.2:p...

NP_000050.2:p.Arg2336His

NP_000050.2:p...

NP_000050.2:p.Arg2336Pro

NP_000050.2:p...

NP_000050.2:p.Arg2336Leu

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#.

38 SubSNP, 2 Frequency, 14 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ICRCG ss35529048 May 24, 2005 (125)
2 PERLEGEN ss69130540 May 17, 2007 (127)
3 ILLUMINA ss74885332 Dec 07, 2007 (129)
4 ILLUMINA ss160595794 Dec 01, 2009 (131)
5 ILLUMINA ss173524662 Jul 04, 2010 (132)
6 BIC_BRODY ss202257683 May 10, 2010 (132)
7 BIC_BRODY ss202257686 May 10, 2010 (132)
8 BIC_BRODY ss202257688 May 10, 2010 (132)
9 ILLUMINA ss480707975 May 04, 2012 (137)
10 ILLUMINA ss480723648 May 04, 2012 (137)
11 ILLUMINA ss481597582 Sep 08, 2015 (146)
12 ILLUMINA ss485148787 May 04, 2012 (137)
13 ILLUMINA ss537144990 Sep 08, 2015 (146)
14 ILLUMINA ss778883568 Sep 08, 2015 (146)
15 ILLUMINA ss783020666 Sep 08, 2015 (146)
16 ILLUMINA ss783980611 Sep 08, 2015 (146)
17 ILLUMINA ss832278182 Sep 08, 2015 (146)
18 ILLUMINA ss834344602 Sep 08, 2015 (146)
19 ILLUMINA ss1752100978 Sep 08, 2015 (146)
20 ILLUMINA ss1959492089 Feb 12, 2016 (147)
21 ILLUMINA ss2633047932 Nov 08, 2017 (151)
22 ILLUMINA ss2635044107 Nov 08, 2017 (151)
23 ILLUMINA ss2710780068 Nov 08, 2017 (151)
24 GNOMAD ss2740354246 Nov 08, 2017 (151)
25 ILLUMINA ss3021497330 Nov 08, 2017 (151)
26 TOPMED ss3189474506 Nov 08, 2017 (151)
27 ILLUMINA ss3627036617 Oct 12, 2018 (152)
28 ILLUMINA ss3631052044 Oct 12, 2018 (152)
29 ILLUMINA ss3633045397 Oct 12, 2018 (152)
30 ILLUMINA ss3633747563 Oct 12, 2018 (152)
31 ILLUMINA ss3634538952 Oct 12, 2018 (152)
32 ILLUMINA ss3635437757 Oct 12, 2018 (152)
33 ILLUMINA ss3636225515 Oct 12, 2018 (152)
34 ILLUMINA ss3637188818 Oct 12, 2018 (152)
35 ILLUMINA ss3638004006 Oct 12, 2018 (152)
36 ILLUMINA ss3640246283 Oct 12, 2018 (152)
37 ILLUMINA ss3642994318 Oct 12, 2018 (152)
38 ILLUMINA ss3651882858 Oct 12, 2018 (152)
39 gnomAD - Exomes NC_000013.10 - 32921033 Oct 12, 2018 (152)
40 TopMed NC_000013.11 - 32346896 Oct 12, 2018 (152)
41 ClinVar RCV000009923.6 Oct 12, 2018 (152)
42 ClinVar RCV000031659.9 Oct 12, 2018 (152)
43 ClinVar RCV000045112.9 Oct 12, 2018 (152)
44 ClinVar RCV000045113.6 Oct 12, 2018 (152)
45 ClinVar RCV000045114.4 Oct 12, 2018 (152)
46 ClinVar RCV000077394.3 Oct 12, 2018 (152)
47 ClinVar RCV000113685.1 Oct 12, 2018 (152)
48 ClinVar RCV000131031.5 Oct 12, 2018 (152)
49 ClinVar RCV000174440.5 Oct 12, 2018 (152)
50 ClinVar RCV000214499.3 Oct 12, 2018 (152)
51 ClinVar RCV000219635.2 Oct 12, 2018 (152)
52 ClinVar RCV000256059.2 Oct 12, 2018 (152)
53 ClinVar RCV000475905.1 Oct 12, 2018 (152)
54 ClinVar RCV000475925.1 Oct 12, 2018 (152)
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
ss480707975, ss2635044107, ss3642994318 NC_000013.9:31819032:G= NC_000013.11:32346895:G= (self)
7599033, ss480723648, ss481597582, ss485148787, ss537144990, ss778883568, ss783020666, ss783980611, ss832278182, ss834344602, ss1752100978, ss1959492089, ss2633047932, ss2710780068, ss2740354246, ss3021497330, ss3627036617, ss3631052044, ss3633045397, ss3633747563, ss3634538952, ss3635437757, ss3636225515, ss3637188818, ss3638004006, ss3640246283, ss3651882858 NC_000013.10:32921032:G= NC_000013.11:32346895:G= (self)
98480827, ss202257683, ss202257686, ss202257688, ss3189474506 NC_000013.11:32346895:G= NC_000013.11:32346895:G= (self)
ss35529048, ss69130540, ss74885332, ss160595794, ss173524662 NT_024524.14:13901032:G= NC_000013.11:32346895:G= (self)
ss480707975, ss2635044107, ss3642994318 NC_000013.9:31819032:G>A NC_000013.11:32346895:G>A (self)
7599033, ss480723648, ss481597582, ss485148787, ss537144990, ss778883568, ss783020666, ss783980611, ss832278182, ss834344602, ss1752100978, ss2633047932, ss2710780068, ss2740354246, ss3627036617, ss3631052044, ss3633045397, ss3633747563, ss3634538952, ss3635437757, ss3636225515, ss3637188818, ss3638004006, ss3640246283 NC_000013.10:32921032:G>A NC_000013.11:32346895:G>A (self)
RCV000009923.6, RCV000031659.9, RCV000045112.9, RCV000131031.5, RCV000174440.5, RCV000475925.1, 98480827, ss202257683, ss3189474506 NC_000013.11:32346895:G>A NC_000013.11:32346895:G>A (self)
ss35529048, ss69130540, ss74885332, ss160595794, ss173524662 NT_024524.14:13901032:G>A NC_000013.11:32346895:G>A (self)
7599033, ss1959492089, ss2740354246, ss3021497330, ss3651882858 NC_000013.10:32921032:G>C NC_000013.11:32346895:G>C (self)
RCV000045113.6, RCV000077394.3, RCV000214499.3, RCV000256059.2, RCV000475905.1, ss202257686 NC_000013.11:32346895:G>C NC_000013.11:32346895:G>C (self)
RCV000045114.4, RCV000113685.1, RCV000219635.2, ss202257688 NC_000013.11:32346895:G>T NC_000013.11:32346895:G>T (self)
Help

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

18 citations for rs28897743
PMID Title Author Year Journal
9536098 Statistical features of human exons and their flanking regions. Zhang MQ et al. 1998 Human molecular genetics
12065746 Biallelic inactivation of BRCA2 in Fanconi anemia. Howlett NG et al. 2002 Science (New York, N.Y.)
15026808 BRCA1 and BRCA2 germline mutation spectrum and frequencies in Belgian breast/ovarian cancer families. Claes K et al. 2004 British journal of cancer
16115142 Inherited FANCD1/BRCA2 exon 7 splice mutations associated with acute myeloid leukaemia in Fanconi anaemia D1 are not found in sporadic childhood leukaemia. Barber LM et al. 2005 British journal of haematology
16792514 A missense mutation in exon 13 in BRCA2, c.7235G>A, results in skipping of exon 13. Thomassen M et al. 2006 Genetic testing
17924331 A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Easton DF et al. 2007 American journal of human genetics
18451181 Functional assays for classification of BRCA2 variants of uncertain significance. Farrugia DJ et al. 2008 Cancer research
18489799 Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer. Machackova E et al. 2008 BMC cancer
20215541 A high proportion of DNA variants of BRCA1 and BRCA2 is associated with aberrant splicing in breast/ovarian cancer patients. Sanz DJ et al. 2010 Clinical cancer research
20960228 Germline mutations in BRCA1 and BRCA2 genes in ethnically diverse high risk families in Israel. Laitman Y et al. 2011 Breast cancer research and treatment
21719596 A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell-based assay. Biswas K et al. 2011 Blood
22505045 Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Houdayer C et al. 2012 Human mutation
22970155 Identification of BRCA1/2 founder mutations in Southern Chinese breast cancer patients using gene sequencing and high resolution DNA melting analysis. Kwong A et al. 2012 PloS one
25395318 Novel and recurrent BRCA2 mutations in Italian breast/ovarian cancer families widen the ovarian cancer cluster region boundaries to exons 13 and 14. Coppa A et al. 2014 Breast cancer research and treatment
25556971 Next-generation sequencing of the BRCA1 and BRCA2 genes for the genetic diagnostics of hereditary breast and/or ovarian cancer. Trujillano D et al. 2015 The Journal of molecular diagnostics
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
26295337 Development and Validation of a Next-Generation Sequencing Assay for BRCA1 and BRCA2 Variants for the Clinical Laboratory. Strom CM et al. 2015 PloS one
26467025 A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. Karbassi I et al. 2016 Human mutation

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.post58+e54ea20