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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.

rs80358439

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr13:32333028 (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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000013 (3/233352, GnomAD_exome)
G=0.000008 (1/120276, ExAC)
G=0.00003 (1/31400, GnomAD) (+ 2 more)
G=0.0001 (1/8980, ALFA Project)
G=0.0002 (1/4480, Estonian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRCA2 : Missense Variant
Publications
4 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.32333028A>G
GRCh38.p12 chr 13 NC_000013.11:g.32333028A>T
GRCh37.p13 chr 13 NC_000013.10:g.32907165A>G
GRCh37.p13 chr 13 NC_000013.10:g.32907165A>T
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.22549A>G
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.22549A>T
Gene: BRCA2, BRCA2 DNA repair associated (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA2 transcript NM_000059.4:c.1550A>G N [AAT] > S [AGT] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.3:p.Asn517Ser N (Asn) > S (Ser) Missense Variant
BRCA2 transcript NM_000059.4:c.1550A>T N [AAT] > I [ATT] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.3:p.Asn517Ile N (Asn) > I (Ile) 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: 46301 )
ClinVar Accession Disease Names Clinical Significance
RCV000031326.9 Breast-ovarian cancer, familial 2 Conflicting-Interpretations-Of-Pathogenicity
RCV000043826.9 Hereditary breast and ovarian cancer syndrome Uncertain-Significance
RCV000129057.5 Hereditary cancer-predisposing syndrome Likely-Benign
RCV000586299.2 not provided Uncertain-Significance
Allele: T (allele ID: 476575 )
ClinVar Accession Disease Names Clinical Significance
RCV000573079.1 Hereditary cancer-predisposing syndrome Uncertain-Significance

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 45494 A=0.99989 G=0.00011
European Sub 34364 A=0.99988 G=0.00012
African Sub 2908 A=1.0000 G=0.0000
African Others Sub 92 A=1.00 G=0.00
African American Sub 2816 A=1.0000 G=0.0000
Asian Sub 164 A=1.000 G=0.000
East Asian Sub 110 A=1.000 G=0.000
Other Asian Sub 54 A=1.00 G=0.00
Latin American 1 Sub 500 A=1.000 G=0.000
Latin American 2 Sub 628 A=1.000 G=0.000
South Asian Sub 94 A=1.00 G=0.00
Other Sub 6836 A=0.9999 G=0.0001


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
gnomAD - Exomes Global Study-wide 233352 A=0.999987 G=0.000013
gnomAD - Exomes European Sub 129744 A=0.999992 G=0.000008
gnomAD - Exomes Asian Sub 43698 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 29690 A=0.99997 G=0.00003
gnomAD - Exomes African Sub 15748 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8924 A=0.9999 G=0.0001
gnomAD - Exomes Other Sub 5548 A=1.0000 G=0.0000
ExAC Global Study-wide 120276 A=0.999992 G=0.000008
ExAC Europe Sub 72828 A=0.99999 G=0.00001
ExAC Asian Sub 24872 A=1.00000 G=0.00000
ExAC American Sub 11538 A=1.00000 G=0.00000
ExAC African Sub 10140 A=1.00000 G=0.00000
ExAC Other Sub 898 A=1.000 G=0.000
gnomAD - Genomes Global Study-wide 31400 A=0.99997 G=0.00003
gnomAD - Genomes European Sub 18904 A=0.99995 G=0.00005
gnomAD - Genomes African Sub 8710 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 1560 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 1088 A=1.0000 G=0.0000
gnomAD - Genomes American Sub 848 A=1.000 G=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=1.000 G=0.000
ALFA Total Global 8980 A=0.9999 G=0.0001
ALFA European Sub 6054 A=1.0000 G=0.0000
ALFA Other Sub 2276 A=0.9996 G=0.0004
ALFA African Sub 594 A=1.000 G=0.000
ALFA Asian Sub 56 A=1.00 G=0.00
ALFA Latin American 1 Sub 0 A=0 G=0
ALFA Latin American 2 Sub 0 A=0 G=0
ALFA South Asian Sub 0 A=0 G=0
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9998 G=0.0002
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.p12 chr 13 NC_000013.11:g.32333028= NC_000013.11:g.32333028A>G NC_000013.11:g.32333028A>T
GRCh37.p13 chr 13 NC_000013.10:g.32907165= NC_000013.10:g.32907165A>G NC_000013.10:g.32907165A>T
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.22549= NG_012772.3:g.22549A>G NG_012772.3:g.22549A>T
BRCA2 transcript NM_000059.4:c.1550= NM_000059.4:c.1550A>G NM_000059.4:c.1550A>T
BRCA2 transcript NM_000059.3:c.1550= NM_000059.3:c.1550A>G NM_000059.3:c.1550A>T
breast cancer type 2 susceptibility protein NP_000050.3:p.Asn517= NP_000050.3:p.Asn517Ser NP_000050.3:p.Asn517Ile
breast cancer type 2 susceptibility protein NP_000050.2:p.Asn517= NP_000050.2:p.Asn517Ser NP_000050.2:p.Asn517Ile
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#.

7 SubSNP, 5 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BIC_BRODY ss202256496 May 10, 2010 (132)
2 EVA_EXAC ss1691250714 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2195324431 Dec 20, 2016 (150)
4 GNOMAD ss2740352806 Nov 08, 2017 (151)
5 GNOMAD ss2749029363 Nov 08, 2017 (151)
6 GNOMAD ss2918246345 Nov 08, 2017 (151)
7 EGCUT_WGS ss3678080139 Jul 13, 2019 (153)
8 Genetic variation in the Estonian population NC_000013.10 - 32907165 Oct 12, 2018 (152)
9 ExAC NC_000013.10 - 32907165 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000013.10 - 32907165 Jul 13, 2019 (153)
11 gnomAD - Exomes NC_000013.10 - 32907165 Jul 13, 2019 (153)
12 dbGaP Population Frequency Project NC_000013.11 - 32333028 Apr 27, 2020 (154)
13 ClinVar RCV000031326.9 Apr 27, 2020 (154)
14 ClinVar RCV000043826.9 Apr 27, 2020 (154)
15 ClinVar RCV000129057.5 Jul 13, 2019 (153)
16 ClinVar RCV000573079.1 Oct 12, 2018 (152)
17 ClinVar RCV000586299.2 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
23818387, 1576350, 165362186, 9595558, ss1691250714, ss2740352806, ss2749029363, ss2918246345, ss3678080139 NC_000013.10:32907164:A:G NC_000013.11:32333027:A:G (self)
RCV000031326.9, RCV000043826.9, RCV000129057.5, RCV000586299.2, 921914009, ss202256496, ss2195324431 NC_000013.11:32333027:A:G NC_000013.11:32333027:A:G (self)
RCV000573079.1 NC_000013.11:32333027:A:T NC_000013.11:32333027: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.

4 citations for rs80358439
PMID Title Author Year Journal
10923033 The breast cancer information core: database design, structure, and scope. Szabo C et al. 2000 Human mutation
18824701 Clinically applicable models to characterize BRCA1 and BRCA2 variants of uncertain significance. Spearman AD et al. 2008 Journal of clinical oncology
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
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
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.post557+f76c771