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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.

rs397507630

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr13:32319253-32319255 (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
delA / dupA
Variation Type
Indel Insertion and 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.32319255delA
GRCh38.p7 chr 13 NC_000013.11:g.32319255dup
GRCh37.p13 chr 13 NC_000013.10:g.32893392delA
GRCh37.p13 chr 13 NC_000013.10:g.32893392dup
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.8776delA
BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.8776dup
Gene: BRCA2, breast cancer 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA2 transcript NM_000059.3:c.246...

NM_000059.3:c.246delA

K [AAA] > K [AA] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Lys...

NP_000050.2:p.Lys82fs

K (Lys) > K (Lys) Frameshift
BRCA2 transcript NM_000059.3:c.246dup E [GAG] > R [AGAG] Coding Sequence Variant
breast cancer type 2 susceptibility protein NP_000050.2:p.Glu...

NP_000050.2:p.Glu83fs

E (Glu) > R (Arg) 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: delA (allele ID: 427341 )
ClinVar Accession Disease Names Clinical Significance
RCV000500205.1 Hereditary breast and ovarian cancer syndrome Pathogenic
Allele: dupA (allele ID: 65961 )
ClinVar Accession Disease Names Clinical Significance
RCV000577454.1 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 AAA= delA dupA Note
GRCh38.p7 chr 13 NC_000013.11:g.32...

NC_000013.11:g.32319253_32319255AAA=

NC_000013.11:g.32...

NC_000013.11:g.32319255delA

NC_000013.11:g.32...

NC_000013.11:g.32319255dup

GRCh37.p13 chr 13 NC_000013.10:g.32...

NC_000013.10:g.32893390_32893392AAA=

NC_000013.10:g.32...

NC_000013.10:g.32893392delA

NC_000013.10:g.32...

NC_000013.10:g.32893392dup

BRCA2 RefSeqGene (LRG_293) NG_012772.3:g.877...

NG_012772.3:g.8774_8776AAA=

NG_012772.3:g.877...

NG_012772.3:g.8776delA

NG_012772.3:g.877...

NG_012772.3:g.8776dup

BRCA2 transcript NM_000059.3:c.244...

NM_000059.3:c.244_246AAA=

NM_000059.3:c.246...

NM_000059.3:c.246delA

NM_000059.3:c.246dup
breast cancer type 2 susceptibility protein NP_000050.2:p.Lys82= NP_000050.2:p.Lys...

NP_000050.2:p.Lys82fs

NP_000050.2:p.Glu...

NP_000050.2:p.Glu83fs

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 ClinVar, 1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss831879389 Nov 05, 2013 (136)
2 ClinVar RCV000500205.1 Jul 20, 2018 (151)
3 ClinVar RCV000577454.1 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
RCV000500205.1 NC_000013.11:32319254:delA NC_000013.11:32319252:delA
RCV000577454.1 NC_000013.11:32319254:dupA NC_000013.11:32319252:dupA
ss831879389 NC_000013.11:32319255:insA NC_000013.11:32319252:dupA (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 rs397507630
PMID Title Author Year Journal
16760289 BRCA1 and BRCA2 genetic testing in Italian breast and/or ovarian cancer families: mutation spectrum and prevalence and analysis of mutation prediction models. Capalbo C et al. 2006 Annals of 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