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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs80359014

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:32362596 (GRCh38.p13) 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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00000 (0/78702, PAGE_STUDY)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRCA2 : Missense Variant
Publications
10 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.p13 chr 13 NC_000013.11:g.32362596A>G
GRCh38.p13 chr 13 NC_000013.11:g.32362596A>T
GRCh37.p13 chr 13 NC_000013.10:g.32936733A>G
GRCh37.p13 chr 13 NC_000013.10:g.32936733A>T
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.52117A>G
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.52117A>T
Gene: BRCA2, BRCA2 DNA repair associated (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA2 transcript NM_000059.4:c.7879A>G I [ATC] > V [GTC] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.3:p.Ile2627Val I (Ile) > V (Val) Missense Variant
BRCA2 transcript NM_000059.4:c.7879A>T I [ATC] > F [TTC] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.3:p.Ile2627Phe I (Ile) > F (Phe) 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: G (allele ID: 151298 )
ClinVar Accession Disease Names Clinical Significance
RCV000130167.3 Hereditary cancer-predisposing syndrome Uncertain-Significance
Allele: T (allele ID: 67098 )
ClinVar Accession Disease Names Clinical Significance
RCV000045337.8 Hereditary breast and ovarian cancer syndrome Pathogenic
RCV000077415.6 Breast-ovarian cancer, familial 2 Pathogenic
RCV000131675.8 Hereditary cancer-predisposing syndrome Pathogenic-Likely-Pathogenic
RCV000218666.10 not provided Pathogenic
RCV000763326.1 Breast-ovarian cancer, familial 2,Familial cancer of breast,Fanconi anemia, complementation group D1,Glioma susceptibility 3,Malignant tumor of prostate,Medulloblastoma,Pancreatic cancer 2,Wilms tumor 1 Pathogenic
RCV001171395.1 not specified Benign
RCV001289537.1 Familial cancer of breast 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
The PAGE Study Global Study-wide 78702 A=1.00000 T=0.00000
The PAGE Study AfricanAmerican Sub 32516 A=1.00000 T=0.00000
The PAGE Study Mexican Sub 10810 A=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 A=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 A=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 A=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 A=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 A=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 A=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 A=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 A=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 A=1.000 T=0.000
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 T
GRCh38.p13 chr 13 NC_000013.11:g.32362596= NC_000013.11:g.32362596A>G NC_000013.11:g.32362596A>T
GRCh37.p13 chr 13 NC_000013.10:g.32936733= NC_000013.10:g.32936733A>G NC_000013.10:g.32936733A>T
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.52117= NG_012772.3:g.52117A>G NG_012772.3:g.52117A>T
BRCA2 transcript NM_000059.4:c.7879= NM_000059.4:c.7879A>G NM_000059.4:c.7879A>T
BRCA2 transcript NM_000059.3:c.7879= NM_000059.3:c.7879A>G NM_000059.3:c.7879A>T
breast cancer type 2 susceptibility protein NP_000050.3:p.Ile2627= NP_000050.3:p.Ile2627Val NP_000050.3:p.Ile2627Phe
breast cancer type 2 susceptibility protein NP_000050.2:p.Ile2627= NP_000050.2:p.Ile2627Val NP_000050.2:p.Ile2627Phe
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#.

8 SubSNP, 1 Frequency, 8 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BIC_BRODY ss202257921 May 10, 2010 (132)
2 CLINVAR ss1457620447 Nov 23, 2014 (142)
3 ILLUMINA ss1959492133 Feb 12, 2016 (147)
4 ILLUMINA ss2710780098 Nov 08, 2017 (151)
5 ILLUMINA ss3021497382 Nov 08, 2017 (151)
6 ILLUMINA ss3651882911 Oct 12, 2018 (152)
7 ILLUMINA ss3725384215 Jul 13, 2019 (153)
8 PAGE_CC ss3771738755 Jul 13, 2019 (153)
9 The PAGE Study NC_000013.11 - 32362596 Jul 13, 2019 (153)
10 ClinVar RCV000045337.8 Apr 27, 2021 (155)
11 ClinVar RCV000077415.6 Apr 27, 2021 (155)
12 ClinVar RCV000130167.3 Apr 27, 2021 (155)
13 ClinVar RCV000131675.8 Apr 27, 2021 (155)
14 ClinVar RCV000218666.10 Apr 27, 2021 (155)
15 ClinVar RCV000763326.1 Jul 13, 2019 (153)
16 ClinVar RCV001171395.1 Apr 27, 2021 (155)
17 ClinVar RCV001289537.1 Apr 27, 2021 (155)
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
RCV000130167.3, ss1457620447 NC_000013.11:32362595:A:G NC_000013.11:32362595:A:G (self)
ss1959492133, ss2710780098, ss3021497382, ss3651882911 NC_000013.10:32936732:A:T NC_000013.11:32362595:A:T (self)
RCV000045337.8, RCV000077415.6, RCV000131675.8, RCV000218666.10, RCV000763326.1, RCV001171395.1, RCV001289537.1, 960224, ss202257921, ss3725384215, ss3771738755 NC_000013.11:32362595:A:T NC_000013.11:32362595:A:T (self)
Help

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

10 citations for rs80359014
PMID Title Author Year Journal
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
19043619 Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Karchin R et al. 2008 Cancer informatics
20104584 Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. Borg A et al. 2010 Human mutation
21990134 A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Lindor NM et al. 2012 Human mutation
23108138 A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity. Guidugli L et al. 2013 Cancer research
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
25948282 New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. Kluska A et al. 2015 BMC medical genomics
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
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad