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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs80359335

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr13:32336937-32336943 (GRCh38.p7) 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
dupA
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRCA2 : Frameshift
Publications
3 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.p7 chr 13 NC_000013.11:g.32336943dup
GRCh37.p13 chr 13 NC_000013.10:g.32911080dup
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.26464dup
Gene: BRCA2, breast cancer 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA2 transcript NM_000059.3:c.258...

NM_000059.3:c.2588dup

N [AAT] > K [AAAT] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Asn...

NP_000050.2:p.Asn863fs

N (Asn) > K (Lys) Frameshift
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: dupA (allele ID: 46349 )
ClinVar Accession Disease Names Clinical Significance
RCV000031374.12 Breast-ovarian cancer, familial 2 Pathogenic
RCV000044019.7 Hereditary breast and ovarian cancer syndrome Pathogenic
RCV000218358.2 Hereditary cancer-predisposing syndrome Pathogenic
RCV000296013.2 not provided 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
Trans-Omics for Precision Medicine Global Study-wide 125568 -

No frequency provided

dupA=0.00001
The Exome Aggregation Consortium Global Study-wide 120148 -

No frequency provided

dupA=0.00002
The Exome Aggregation Consortium Europe Sub 72780 -

No frequency provided

dupA=0.0000
The Exome Aggregation Consortium Asian Sub 24924 -

No frequency provided

dupA=0.0000
The Exome Aggregation Consortium American Sub 11446 -

No frequency provided

dupA=0.0000
The Exome Aggregation Consortium African Sub 10106 -

No frequency provided

dupA=0.0000
The Exome Aggregation Consortium Other Sub 892 -

No frequency provided

dupA=0.00
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)7= dupA Note
GRCh38.p7 chr 13 NC_000013.11:g.32336937...

NC_000013.11:g.32336937_32336943AAAAAAA=

NC_000013.11:g.32336943dup
GRCh37.p13 chr 13 NC_000013.10:g.32911074...

NC_000013.10:g.32911074_32911080AAAAAAA=

NC_000013.10:g.32911080dup
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.26458_264...

NG_012772.3:g.26458_26464AAAAAAA=

NG_012772.3:g.26464dup
BRCA2 transcript NM_000059.3:c.2582_2588...

NM_000059.3:c.2582_2588AAAAAAA=

NM_000059.3:c.2588dup
breast cancer type 2 susceptibility protein NP_000050.2:p.Gln861_As...

NP_000050.2:p.Gln861_Asn863=

NP_000050.2:p.Asn863fs
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#.

2 Frequency, 7 SubSNP, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BIC_BRODY ss204139408 Mar 10, 2010 (132)
2 BIC_BRODY ss204139419 Mar 10, 2010 (136)
3 CLINVAR ss831879391 Nov 05, 2013 (136)
4 CLINVAR ss1518728550 Dec 11, 2014 (136)
5 EVA_EXAC ss1712035586 Apr 01, 2015 (136)
6 ILLUMINA ss3021497121 Nov 08, 2017 (151)
7 TOPMED ss3189472874 Nov 08, 2017 (151)
8 The Exome Aggregation Consortium NC_000013.10 - 32911074 Jul 20, 2018 (151)
9 Trans-Omics for Precision Medicine NC_000013.11 - 32336937 Jul 20, 2018 (151)
10 ClinVar RCV000031374.12 Jul 20, 2018 (151)
11 ClinVar RCV000044019.7 Jul 20, 2018 (151)
12 ClinVar RCV000218358.2 Jul 20, 2018 (151)
13 ClinVar RCV000296013.2 Jul 20, 2018 (151)
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).

Associated ID History Updated (Build)
rs80359338 May 11, 2017 (136)
rs606231399 May 11, 2017 (136)
rs768104789 Feb 27, 2017 (136)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
1576529, ss1712035586, ss3021497121 NC_000013.10:32911073:insA NC_000013.11:32336936:dupA (self) , rs1357556348
98479369, ss3189472874 NC_000013.11:32336936:insA NC_000013.11:32336936:dupA rs1357556348
ss204139408 NC_000013.11:32336937:insA NC_000013.11:32336936:dupA (self)
ss1518728550 NC_000013.11:32336938:insA NC_000013.11:32336936:dupA (self)
RCV000031374.12, RCV000044019.7, RCV000218358.2, RCV000296013.2 NC_000013.11:32336942:dupA NC_000013.11:32336936:dupA
ss204139419, ss831879391 NC_000013.11:32336943:insA NC_000013.11:32336936:dupA (self)
Help

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

3 citations for rs80359335
PMID Title Author Year Journal
11030417 Prevalence of BRCA1 and BRCA2 mutations among clinic-based African American families with breast cancer. Gao Q et al. 2000 Human genetics
21324516 Frequencies of BRCA1 and BRCA2 mutations among 1,342 unselected patients with invasive ovarian cancer. Zhang S et al. 2011 Gynecologic oncology
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

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: 0.1.4.post833+d3ba21e