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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.

rs461080

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr21:13029724 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000406 (57/140256, GnomAD)
T=0.40895 (6854/16760, 8.3KJPN)
T=0.4991 (2233/4474, ALFA) (+ 3 more)
T=0.4137 (1212/2930, KOREAN)
T=0.448 (250/558, SGDP_PRJ)
T=0.477 (103/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 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 21 NC_000021.9:g.13029724T>A
GRCh38.p13 chr 21 NC_000021.9:g.13029724T>C
GRCh38.p13 chr 21 NC_000021.9:g.13029724T>G
GRCh37.p13 chr 21 NC_000021.8:g.14402045T>A
GRCh37.p13 chr 21 NC_000021.8:g.14402045T>C
GRCh37.p13 chr 21 NC_000021.8:g.14402045T>G
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 4474 T=0.4991 C=0.5009, G=0.0000
European Sub 4466 T=0.4991 C=0.5009, G=0.0000
African Sub 0 T=0 C=0, G=0
African Others Sub 0 T=0 C=0, G=0
African American Sub 0 T=0 C=0, G=0
Asian Sub 0 T=0 C=0, G=0
East Asian Sub 0 T=0 C=0, G=0
Other Asian Sub 0 T=0 C=0, G=0
Latin American 1 Sub 0 T=0 C=0, G=0
Latin American 2 Sub 0 T=0 C=0, G=0
South Asian Sub 0 T=0 C=0, G=0
Other Sub 8 T=0.5 C=0.5, G=0.0


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
gnomAD - Genomes Global Study-wide 140256 T=0.999594 G=0.000406
gnomAD - Genomes European Sub 75946 T=1.00000 G=0.00000
gnomAD - Genomes African Sub 42030 T=0.99869 G=0.00131
gnomAD - Genomes American Sub 13668 T=0.99985 G=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 T=1.0000 G=0.0000
8.3KJPN JAPANESE Study-wide 16760 T=0.40895 C=0.59105
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.4137 A=0.0000, C=0.5863, G=0.0000
SGDP_PRJ Global Study-wide 558 T=0.448 C=0.552
Qatari Global Study-wide 216 T=0.477 C=0.523
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= A C G
GRCh38.p13 chr 21 NC_000021.9:g.13029724= NC_000021.9:g.13029724T>A NC_000021.9:g.13029724T>C NC_000021.9:g.13029724T>G
GRCh37.p13 chr 21 NC_000021.8:g.14402045= NC_000021.8:g.14402045T>A NC_000021.8:g.14402045T>C NC_000021.8:g.14402045T>G
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#.

34 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss623220 Jul 16, 2000 (80)
2 PERLEGEN ss3995652 Sep 28, 2001 (100)
3 WUGSC_SSAHASNP ss14445691 Dec 05, 2003 (119)
4 SC_SNP ss14759905 Dec 05, 2003 (119)
5 SSAHASNP ss21822703 Apr 05, 2004 (121)
6 ABI ss43530876 Mar 13, 2006 (126)
7 HGSV ss80678631 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss91766935 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss95879463 Feb 04, 2009 (130)
10 ILLUMINA-UK ss117448637 Feb 14, 2009 (130)
11 ENSEMBL ss135656474 Dec 01, 2009 (131)
12 ENSEMBL ss138282174 Dec 01, 2009 (131)
13 GMI ss156667181 Dec 01, 2009 (131)
14 BL ss255839443 May 09, 2011 (134)
15 GMI ss283460551 May 04, 2012 (137)
16 GMI ss287493202 Apr 25, 2013 (138)
17 SSMP ss662271557 Apr 25, 2013 (138)
18 DDI ss1429120919 Apr 01, 2015 (144)
19 WEILL_CORNELL_DGM ss1938466810 Feb 12, 2016 (147)
20 GENOMED ss1969175420 Jul 19, 2016 (147)
21 GRF ss2704318633 Nov 08, 2017 (151)
22 GNOMAD ss2969714863 Nov 08, 2017 (151)
23 SWEGEN ss3018580638 Nov 08, 2017 (151)
24 CSHL ss3352626230 Nov 08, 2017 (151)
25 TOPMED ss3366041671 Nov 08, 2017 (151)
26 TOPMED ss3366041672 Nov 08, 2017 (151)
27 URBANLAB ss3651071948 Oct 12, 2018 (152)
28 PACBIO ss3788708708 Jul 13, 2019 (153)
29 PACBIO ss3793590005 Jul 13, 2019 (153)
30 PACBIO ss3798476227 Jul 13, 2019 (153)
31 KHV_HUMAN_GENOMES ss3822037931 Jul 13, 2019 (153)
32 SGDP_PRJ ss3889594327 Apr 27, 2020 (154)
33 KRGDB ss3939994335 Apr 27, 2020 (154)
34 TOMMO_GENOMICS ss5230697167 Apr 26, 2021 (155)
35 gnomAD - Genomes NC_000021.9 - 13029724 Apr 26, 2021 (155)
36 KOREAN population from KRGDB NC_000021.8 - 14402045 Apr 27, 2020 (154)
37 Qatari NC_000021.8 - 14402045 Apr 27, 2020 (154)
38 SGDP_PRJ NC_000021.8 - 14402045 Apr 27, 2020 (154)
39 8.3KJPN NC_000021.8 - 14402045 Apr 26, 2021 (155)
40 ALFA NC_000021.9 - 13029724 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).

Associated ID History Updated (Build)
rs57615024 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
47171729, ss3939994335 NC_000021.8:14402044:T:A NC_000021.9:13029723:T:A (self)
ss80678631, ss91766935, ss117448637, ss255839443, ss283460551, ss287493202 NC_000021.7:13323915:T:C NC_000021.9:13029723:T:C (self)
47171729, 20508732, 41611307, 88666474, ss662271557, ss1429120919, ss1938466810, ss1969175420, ss2704318633, ss2969714863, ss3018580638, ss3352626230, ss3788708708, ss3793590005, ss3798476227, ss3889594327, ss3939994335, ss5230697167 NC_000021.8:14402044:T:C NC_000021.9:13029723:T:C (self)
11055129616, ss3366041671, ss3651071948, ss3822037931 NC_000021.9:13029723:T:C NC_000021.9:13029723:T:C (self)
ss14445691, ss14759905, ss21822703 NT_011512.9:63915:T:C NC_000021.9:13029723:T:C (self)
ss623220, ss3995652, ss43530876, ss95879463, ss135656474, ss138282174, ss156667181 NT_011512.11:63915:T:C NC_000021.9:13029723:T:C (self)
47171729, ss2969714863, ss3939994335 NC_000021.8:14402044:T:G NC_000021.9:13029723:T:G (self)
557946308, 11055129616, ss3366041672 NC_000021.9:13029723:T:G NC_000021.9:13029723:T:G (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 rs461080

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