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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1476316387

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:61295083 (GRCh38.p14) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000121 (32/264690, TOPMED)
A=0.000071 (10/140160, GnomAD)
A=0.00131 (37/28252, 14KJPN) (+ 7 more)
A=0.00149 (25/16752, 8.3KJPN)
A=0.00007 (1/14050, ALFA)
A=0.0005 (3/6404, 1000G_30x)
A=0.0038 (11/2908, KOREAN)
A=0.0039 (7/1778, Korea1K)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
VWCE : Non Coding Transcript Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 G=0.99993 A=0.00007 0.999858 0.0 0.000142 0
European Sub 9690 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=0.998 A=0.002 0.995968 0.0 0.004032 0


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
TopMed Global Study-wide 264690 G=0.999879 A=0.000121
gnomAD - Genomes Global Study-wide 140160 G=0.999929 A=0.000071
gnomAD - Genomes European Sub 75874 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42030 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13654 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3126 G=0.9968 A=0.0032
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
14KJPN JAPANESE Study-wide 28252 G=0.99869 A=0.00131
8.3KJPN JAPANESE Study-wide 16752 G=0.99851 A=0.00149
Allele Frequency Aggregator Total Global 14050 G=0.99993 A=0.00007
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=0.998 A=0.002
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9995 A=0.0005
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9974 A=0.0026
1000Genomes_30x American Sub 980 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2908 G=0.9962 A=0.0038
Korean Genome Project KOREAN Study-wide 1778 G=0.9961 A=0.0039
SGDP_PRJ Global Study-wide 2 G=0.5 A=0.5
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.p14 chr 11 NC_000011.10:g.61295083G>A
GRCh37.p13 chr 11 NC_000011.9:g.61062555G>A
Gene: VWCE, von Willebrand factor C and EGF domains (minus strand)
Molecule type Change Amino acid[Codon] SO Term
VWCE transcript NM_152718.2:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X1 XM_006718460.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X4 XM_006718462.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X5 XM_011544817.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X2 XM_017017341.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X11 XM_017017344.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X3 XM_047426550.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X6 XM_047426551.1:c.-46= N/A 5 Prime UTR Variant
VWCE transcript variant X7 XM_017017342.2:c.-341= N/A 5 Prime UTR Variant
VWCE transcript variant X8 XM_047426552.1:c.-341= N/A 5 Prime UTR Variant
VWCE transcript variant X9 XM_047426553.1:c. N/A Genic Upstream Transcript Variant
VWCE transcript variant X10 XR_949822.3:n.234C>T 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.

Not Reported in ClinVar
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= A
GRCh38.p14 chr 11 NC_000011.10:g.61295083= NC_000011.10:g.61295083G>A
GRCh37.p13 chr 11 NC_000011.9:g.61062555= NC_000011.9:g.61062555G>A
VWCE transcript variant X10 XR_949822.3:n.234= XR_949822.3:n.234C>T
VWCE transcript variant X7 XR_949822.2:n.234= XR_949822.2:n.234C>T
VWCE transcript variant X8 XR_949822.1:n.234= XR_949822.1:n.234C>T
VWCE transcript NM_152718.2:c.-46= NM_152718.2:c.-46C>T
VWCE transcript variant X7 XM_017017342.2:c.-341= XM_017017342.2:c.-341C>T
VWCE transcript variant X1 XM_006718460.1:c.-46= XM_006718460.1:c.-46C>T
VWCE transcript variant X2 XM_017017341.1:c.-46= XM_017017341.1:c.-46C>T
VWCE transcript variant X3 XM_047426550.1:c.-46= XM_047426550.1:c.-46C>T
VWCE transcript variant X4 XM_006718462.1:c.-46= XM_006718462.1:c.-46C>T
VWCE transcript variant X8 XM_047426552.1:c.-341= XM_047426552.1:c.-341C>T
VWCE transcript variant X5 XM_011544817.1:c.-46= XM_011544817.1:c.-46C>T
VWCE transcript variant X6 XM_047426551.1:c.-46= XM_047426551.1:c.-46C>T
VWCE transcript variant X11 XM_017017344.1:c.-46= XM_017017344.1:c.-46C>T
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#.

13 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2739020819 Nov 08, 2017 (151)
2 GNOMAD ss2748628570 Nov 08, 2017 (151)
3 GNOMAD ss2900321932 Nov 08, 2017 (151)
4 EVA ss3749369632 Jul 13, 2019 (153)
5 SGDP_PRJ ss3876380894 Apr 26, 2020 (154)
6 KRGDB ss3924742502 Apr 26, 2020 (154)
7 KOGIC ss3970010230 Apr 26, 2020 (154)
8 TOPMED ss4887299893 Apr 26, 2021 (155)
9 TOMMO_GENOMICS ss5202242184 Apr 26, 2021 (155)
10 1000G_HIGH_COVERAGE ss5287624385 Oct 16, 2022 (156)
11 EVA ss5399942149 Oct 16, 2022 (156)
12 1000G_HIGH_COVERAGE ss5583453317 Oct 16, 2022 (156)
13 TOMMO_GENOMICS ss5750196373 Oct 16, 2022 (156)
14 1000Genomes_30x NC_000011.10 - 61295083 Oct 16, 2022 (156)
15 gnomAD - Genomes NC_000011.10 - 61295083 Apr 26, 2021 (155)
16 KOREAN population from KRGDB NC_000011.9 - 61062555 Apr 26, 2020 (154)
17 Korean Genome Project NC_000011.10 - 61295083 Apr 26, 2020 (154)
18 SGDP_PRJ NC_000011.9 - 61062555 Apr 26, 2020 (154)
19 8.3KJPN NC_000011.9 - 61062555 Apr 26, 2021 (155)
20 14KJPN NC_000011.10 - 61295083 Oct 16, 2022 (156)
21 TopMed NC_000011.10 - 61295083 Apr 26, 2021 (155)
22 ALFA NC_000011.10 - 61295083 Apr 26, 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
31919896, 28397874, 60211491, ss2739020819, ss2748628570, ss2900321932, ss3749369632, ss3876380894, ss3924742502, ss5202242184, ss5399942149 NC_000011.9:61062554:G:A NC_000011.10:61295082:G:A (self)
70979252, 381428872, 26388231, 84033477, 102845549, 8491675098, ss3970010230, ss4887299893, ss5287624385, ss5583453317, ss5750196373 NC_000011.10:61295082:G:A NC_000011.10:61295082:G:A (self)
Help

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

No publications for rs1476316387

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.post820+afb47a3d