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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.

rs461410

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr21:13021806 (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
A>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000009 (1/115360, GnomAD)
A=0.49922 (8367/16760, 8.3KJPN)
C=0.2867 (1505/5250, ALFA) (+ 4 more)
C=0.4856 (1419/2922, KOREAN)
C=0.087 (87/998, GoNL)
A=0.454 (166/366, SGDP_PRJ)
C=0.162 (35/216, 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.13021806A>C
GRCh38.p13 chr 21 NC_000021.9:g.13021806A>T
GRCh37.p13 chr 21 NC_000021.8:g.14394127A>C
GRCh37.p13 chr 21 NC_000021.8:g.14394127A>T
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 5250 A=0.7133 C=0.2867, T=0.0000
European Sub 5116 A=0.7064 C=0.2936, T=0.0000
African Sub 38 A=1.00 C=0.00, T=0.00
African Others Sub 0 A=0 C=0, T=0
African American Sub 38 A=1.00 C=0.00, T=0.00
Asian Sub 4 A=1.0 C=0.0, T=0.0
East Asian Sub 4 A=1.0 C=0.0, T=0.0
Other Asian Sub 0 A=0 C=0, T=0
Latin American 1 Sub 16 A=1.00 C=0.00, T=0.00
Latin American 2 Sub 42 A=1.00 C=0.00, T=0.00
South Asian Sub 6 A=1.0 C=0.0, T=0.0
Other Sub 28 A=0.89 C=0.11, T=0.00


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 115360 A=0.999991 T=0.000009
gnomAD - Genomes European Sub 62454 A=0.99998 T=0.00002
gnomAD - Genomes African Sub 34524 A=1.00000 T=0.00000
gnomAD - Genomes American Sub 11160 A=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 2804 A=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 2666 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1752 A=1.0000 T=0.0000
8.3KJPN JAPANESE Study-wide 16760 A=0.49922 C=0.50078
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.5144 C=0.4856
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.913 C=0.087
SGDP_PRJ Global Study-wide 366 A=0.454 C=0.544, T=0.003
Qatari Global Study-wide 216 A=0.838 C=0.162
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 A= C T
GRCh38.p13 chr 21 NC_000021.9:g.13021806= NC_000021.9:g.13021806A>C NC_000021.9:g.13021806A>T
GRCh37.p13 chr 21 NC_000021.8:g.14394127= NC_000021.8:g.14394127A>C NC_000021.8:g.14394127A>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#.

26 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss623857 Jul 16, 2000 (80)
2 TSC-CSHL ss3006980 Jun 15, 2001 (123)
3 PERLEGEN ss3995636 Sep 28, 2001 (123)
4 TSC-CSHL ss5533308 Oct 10, 2002 (123)
5 WUGSC_SSAHASNP ss14439910 Dec 05, 2003 (123)
6 SSAHASNP ss35510356 May 24, 2005 (125)
7 ENSEMBL ss143631443 Dec 01, 2009 (147)
8 1000GENOMES ss237904858 Jul 15, 2010 (132)
9 GMI ss283460430 May 04, 2012 (137)
10 SSMP ss662271441 Apr 25, 2013 (138)
11 EVA-GONL ss994917079 Aug 21, 2014 (142)
12 DDI ss1429120842 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1938466631 Feb 12, 2016 (147)
14 GRF ss2704318465 Nov 08, 2017 (151)
15 GNOMAD ss2969713093 Nov 08, 2017 (151)
16 SWEGEN ss3018580286 Nov 08, 2017 (151)
17 TOPMED ss3366037855 Nov 08, 2017 (151)
18 TOPMED ss3366037856 Nov 08, 2017 (151)
19 URBANLAB ss3651071892 Oct 12, 2018 (152)
20 EVA ss3758882037 Jul 13, 2019 (153)
21 PACBIO ss3788708622 Jul 13, 2019 (153)
22 PACBIO ss3793589922 Jul 13, 2019 (153)
23 PACBIO ss3798476155 Jul 13, 2019 (153)
24 SGDP_PRJ ss3889593945 Apr 27, 2020 (154)
25 KRGDB ss3939993817 Apr 27, 2020 (154)
26 TOMMO_GENOMICS ss5230696345 Apr 26, 2021 (155)
27 gnomAD - Genomes NC_000021.9 - 13021806 Apr 26, 2021 (155)
28 Genome of the Netherlands Release 5 NC_000021.8 - 14394127 Apr 27, 2020 (154)
29 KOREAN population from KRGDB NC_000021.8 - 14394127 Apr 27, 2020 (154)
30 Qatari NC_000021.8 - 14394127 Apr 27, 2020 (154)
31 SGDP_PRJ NC_000021.8 - 14394127 Apr 27, 2020 (154)
32 8.3KJPN NC_000021.8 - 14394127 Apr 26, 2021 (155)
33 ALFA NC_000021.9 - 13021806 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)
rs2090038 Sep 24, 2004 (123)
rs2821578 Feb 20, 2003 (111)
rs4107568 Dec 16, 2002 (110)
rs79382921 Jul 19, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35510356, ss283460430 NC_000021.7:13315997:A:C NC_000021.9:13021805:A:C (self)
19480926, 47171211, 20508553, 41610925, 88665652, ss237904858, ss662271441, ss994917079, ss1429120842, ss1938466631, ss2704318465, ss2969713093, ss3018580286, ss3758882037, ss3788708622, ss3793589922, ss3798476155, ss3889593945, ss3939993817, ss5230696345 NC_000021.8:14394126:A:C NC_000021.9:13021805:A:C (self)
6000614191, ss3366037855, ss3651071892 NC_000021.9:13021805:A:C NC_000021.9:13021805:A:C (self)
ss14439910 NT_011512.9:55997:A:C NC_000021.9:13021805:A:C (self)
ss623857, ss3006980, ss3995636, ss5533308, ss143631443 NT_011512.11:55997:A:C NC_000021.9:13021805:A:C (self)
41610925, ss3889593945 NC_000021.8:14394126:A:T NC_000021.9:13021805:A:T (self)
557943183, 6000614191, ss3366037856 NC_000021.9:13021805:A:T NC_000021.9:13021805:A:T (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 rs461410

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