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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.

rs80357908

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:43094021 (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
delG
Variation Type
Deletion
Frequency
delG=0.000004 (1/251044, GnomAD_exome)
delG=0.000008 (1/121170, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRCA1 : Frameshift Variant
Publications
2 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 17 NC_000017.11:g.43094021del
GRCh37.p13 chr 17 NC_000017.10:g.41246038del
BRCA1 RefSeqGene (LRG_292) NG_005905.2:g.123963del
Gene: BRCA1, BRCA1 DNA repair associated (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BRCA1 transcript variant 4 NM_007298.3:c.787+723del N/A Intron Variant
BRCA1 transcript variant 5 NM_007299.4:c.787+723del N/A Intron Variant
BRCA1 transcript variant 3 NM_007297.4:c.1369del R [CGT] > V [GT] Coding Sequence Variant
breast cancer type 1 susceptibility protein isoform 3 NP_009228.2:p.Arg457fs R (Arg) > V (Val) Frameshift Variant
BRCA1 transcript variant 2 NM_007300.4:c.1510del R [CGT] > V [GT] Coding Sequence Variant
breast cancer type 1 susceptibility protein isoform 2 NP_009231.2:p.Arg504fs R (Arg) > V (Val) Frameshift Variant
BRCA1 transcript variant 1 NM_007294.4:c.1510del R [CGT] > V [GT] Coding Sequence Variant
breast cancer type 1 susceptibility protein isoform 1 NP_009225.1:p.Arg504fs R (Arg) > V (Val) Frameshift Variant
BRCA1 transcript variant 6 NR_027676.2:n.1687del N/A Non Coding Transcript 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: delG (allele ID: 45974 )
ClinVar Accession Disease Names Clinical Significance
RCV000030999.6 Breast-ovarian cancer, familial 1 Pathogenic
RCV000130024.4 Hereditary cancer-predisposing syndrome Pathogenic
RCV000496881.3 Hereditary breast and ovarian cancer syndrome Pathogenic
RCV000985369.1 not provided Pathogenic
RCV001270965.1 Breast and/or ovarian cancer 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
gnomAD - Exomes Global Study-wide 251044 G=0.999996 delG=0.000004
gnomAD - Exomes European Sub 135072 G=0.999993 delG=0.000007
gnomAD - Exomes Asian Sub 48978 G=1.00000 delG=0.00000
gnomAD - Exomes American Sub 34552 G=1.00000 delG=0.00000
gnomAD - Exomes African Sub 16250 G=1.00000 delG=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=1.00000 delG=0.00000
gnomAD - Exomes Other Sub 6116 G=1.0000 delG=0.0000
ExAC Global Study-wide 121170 G=0.999992 delG=0.000008
ExAC Europe Sub 73214 G=0.99999 delG=0.00001
ExAC Asian Sub 25122 G=1.00000 delG=0.00000
ExAC American Sub 11536 G=1.00000 delG=0.00000
ExAC African Sub 10394 G=1.00000 delG=0.00000
ExAC Other Sub 904 G=1.000 delG=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 G= delG
GRCh38.p13 chr 17 NC_000017.11:g.43094021= NC_000017.11:g.43094021del
GRCh37.p13 chr 17 NC_000017.10:g.41246038= NC_000017.10:g.41246038del
BRCA1 RefSeqGene (LRG_292) NG_005905.2:g.123963= NG_005905.2:g.123963del
BRCA1 transcript variant 2 NM_007300.4:c.1510= NM_007300.4:c.1510del
BRCA1 transcript variant 2 NM_007300.3:c.1510= NM_007300.3:c.1510del
BRCA1 transcript variant 1 NM_007294.4:c.1510= NM_007294.4:c.1510del
BRCA1 transcript variant 1 NM_007294.3:c.1510= NM_007294.3:c.1510del
BRCA1 transcript variant 3 NM_007297.4:c.1369= NM_007297.4:c.1369del
BRCA1 transcript variant 3 NM_007297.3:c.1369= NM_007297.3:c.1369del
BRCA1 transcript variant 6 NR_027676.2:n.1687= NR_027676.2:n.1687del
BRCA1 transcript variant 6 NR_027676.1:n.1646= NR_027676.1:n.1646del
BRCA1 transcript variant BRCA1b NM_007295.2:c.1510= NM_007295.2:c.1510del
BRCA1 transcript variant BRCA1-exon4 NM_007306.2:c.*1446= NM_007306.2:c.*1446del
BRCA1 transcript variant BRCA1a' NM_007296.2:c.1510= NM_007296.2:c.1510del
BRCA1 transcript variant BRCA1-delta9-10 NM_007302.2:c.1387= NM_007302.2:c.1387del
BRCA1 transcript variant BRCA1-delta15-17 NM_007301.2:c.1510= NM_007301.2:c.1510del
BRCA1 transcript variant BRCA1b NM_007295.1:c.1510= NM_007295.1:c.1510del
BRCA1 transcript variant BRCA1-exon4 NM_007306.1:c.*1446= NM_007306.1:c.*1446del
BRCA1 transcript variant BRCA1a' NM_007296.1:c.1510= NM_007296.1:c.1510del
BRCA1 transcript variant BRCA1-delta9-10 NM_007302.1:c.1387= NM_007302.1:c.1387del
BRCA1 transcript variant BRCA1-delta15-17 NM_007301.1:c.1510= NM_007301.1:c.1510del
breast cancer type 1 susceptibility protein isoform 2 NP_009231.2:p.Arg504= NP_009231.2:p.Arg504fs
breast cancer type 1 susceptibility protein isoform 1 NP_009225.1:p.Arg504= NP_009225.1:p.Arg504fs
breast cancer type 1 susceptibility protein isoform 3 NP_009228.2:p.Arg457= NP_009228.2:p.Arg457fs
BRCA1 transcript variant 4 NM_007298.3:c.787+723= NM_007298.3:c.787+723del
BRCA1 transcript variant 5 NM_007299.3:c.787+723= NM_007299.3:c.787+723del
BRCA1 transcript variant 5 NM_007299.4:c.787+723= NM_007299.4:c.787+723del
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 SubSNP, 2 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BIC_BRODY ss187450885 May 08, 2010 (132)
2 EVA_EXAC ss1712145807 Apr 01, 2015 (144)
3 ExAC NC_000017.10 - 41246038 Oct 12, 2018 (152)
4 gnomAD - Exomes NC_000017.10 - 41246038 Jul 13, 2019 (153)
5 ClinVar RCV000030999.6 Oct 12, 2018 (152)
6 ClinVar RCV000130024.4 Apr 27, 2021 (155)
7 ClinVar RCV000496881.3 Oct 12, 2018 (152)
8 ClinVar RCV000985369.1 Apr 27, 2020 (154)
9 ClinVar RCV001270965.1 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
3247011, 12057382, ss1712145807 NC_000017.10:41246037:G: NC_000017.11:43094020:G: (self)
RCV000030999.6, RCV000130024.4, RCV000496881.3, RCV000985369.1, RCV001270965.1, ss187450885 NC_000017.11:43094020:G: NC_000017.11:43094020:G: (self)
Help

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

2 citations for rs80357908
PMID Title Author Year Journal
18489799 Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer. Machackova E et al. 2008 BMC cancer
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.post596+ae089ad