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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.

rs397507889

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr13:32346885 (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
delT
Variation Type
Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRCA2 : Frameshift
Publications
1 citation
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.32346885delT
GRCh37.p13 chr 13 NC_000013.10:g.32921022delT
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.36406delT
Gene: BRCA2, breast cancer 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA2 transcript NM_000059.3:c.699...

NM_000059.3:c.6996delT

C [TGT] > W [TG] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Cys...

NP_000050.2:p.Cys2332fs

C (Cys) > W (Trp) 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: delT (allele ID: 66902 )
ClinVar Accession Disease Names Clinical Significance
RCV000577724.1 Familial cancer of breast Not-Provided
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").

None
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 T= delT Note
GRCh38.p7 chr 13 NC_000013.11:g.32346885T= NC_000013.11:g.32346885...

NC_000013.11:g.32346885delT

GRCh37.p13 chr 13 NC_000013.10:g.32921022T= NC_000013.10:g.32921022...

NC_000013.10:g.32921022delT

BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.36406T= NG_012772.3:g.36406delT
BRCA2 transcript NM_000059.3:c.6996T= NM_000059.3:c.6996delT
breast cancer type 2 susceptibility protein NP_000050.2:p.Cys2332= NP_000050.2:p.Cys2332fs
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#.

1 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss831879697 Nov 05, 2013 (136)
2 ClinVar RCV000577724.1 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
1577421, 51948831, 9368977, ss1691251684, ss2740354242, ss2749029734, ss2918247307 NC_000013.10:32921021:T= NC_000013.11:32346884:T= rs779498845
98480824, ss831879697, ss1751109788, ss3189474503 NC_000013.11:32346884:T= NC_000013.11:32346884:T= (self) , rs779498845
RCV000577724.1, ss831879697 NC_000013.11:32346884:delT NC_000013.11:32346884:delT (self)
Help

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

1 citation for rs397507889
PMID Title Author Year Journal
21324516 Frequencies of BRCA1 and BRCA2 mutations among 1,342 unselected patients with invasive ovarian cancer. Zhang S et al. 2011 Gynecologic oncology

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