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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.

rs4809316

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:63632195 (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
C>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.02284 (726/31786, GnomAD)
A=0.01936 (533/27530, 14KJPN)
A=0.03938 (645/16378, 8.3KJPN) (+ 7 more)
C=0.49469 (5868/11862, ALFA)
A=0.4265 (2136/5008, 1000G)
A=0.0916 (267/2916, KOREAN)
A=0.0393 (71/1806, Korea1K)
A=0.093 (46/492, NorthernSweden)
C=0.340 (96/282, SGDP_PRJ)
C=0.38 (13/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 C=0.49469 A=0.50531
European Sub 7618 C=0.4269 A=0.5731
African Sub 2816 C=0.6349 A=0.3651
African Others Sub 108 C=0.713 A=0.287
African American Sub 2708 C=0.6318 A=0.3682
Asian Sub 108 C=0.917 A=0.083
East Asian Sub 84 C=0.92 A=0.08
Other Asian Sub 24 C=0.92 A=0.08
Latin American 1 Sub 146 C=0.473 A=0.527
Latin American 2 Sub 610 C=0.561 A=0.439
South Asian Sub 94 C=0.68 A=0.32
Other Sub 470 C=0.540 A=0.460


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 31786 C=0.97716 A=0.02284
gnomAD - Genomes African Sub 13492 C=0.98762 A=0.01238
gnomAD - Genomes European Sub 12166 C=0.96112 A=0.03888
gnomAD - Genomes American Sub 3236 C=0.9892 A=0.0108
gnomAD - Genomes East Asian Sub 2002 C=0.9875 A=0.0125
gnomAD - Genomes Other Sub 486 C=0.973 A=0.027
gnomAD - Genomes Ashkenazi Jewish Sub 404 C=0.968 A=0.032
14KJPN JAPANESE Study-wide 27530 C=0.98064 A=0.01936
8.3KJPN JAPANESE Study-wide 16378 C=0.96062 A=0.03938
Allele Frequency Aggregator Total Global 11862 C=0.49469 A=0.50531
Allele Frequency Aggregator European Sub 7618 C=0.4269 A=0.5731
Allele Frequency Aggregator African Sub 2816 C=0.6349 A=0.3651
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.561 A=0.439
Allele Frequency Aggregator Other Sub 470 C=0.540 A=0.460
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.473 A=0.527
Allele Frequency Aggregator Asian Sub 108 C=0.917 A=0.083
Allele Frequency Aggregator South Asian Sub 94 C=0.68 A=0.32
1000Genomes Global Study-wide 5008 C=0.5735 A=0.4265
1000Genomes African Sub 1322 C=0.5832 A=0.4168
1000Genomes East Asian Sub 1008 C=0.7708 A=0.2292
1000Genomes Europe Sub 1006 C=0.3608 A=0.6392
1000Genomes South Asian Sub 978 C=0.643 A=0.357
1000Genomes American Sub 694 C=0.478 A=0.522
KOREAN population from KRGDB KOREAN Study-wide 2916 C=0.9084 A=0.0916
Korean Genome Project KOREAN Study-wide 1806 C=0.9607 A=0.0393
Northern Sweden ACPOP Study-wide 492 C=0.907 A=0.093
SGDP_PRJ Global Study-wide 282 C=0.340 A=0.660
Siberian Global Study-wide 34 C=0.38 A=0.62
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 20 NC_000020.11:g.63632195C>A
GRCh37.p13 chr 20 NC_000020.10:g.62263548C>A
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 C= A
GRCh38.p14 chr 20 NC_000020.11:g.63632195= NC_000020.11:g.63632195C>A
GRCh37.p13 chr 20 NC_000020.10:g.62263548= NC_000020.10:g.62263548C>A
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#.

24 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6638098 Feb 20, 2003 (111)
2 SC_SNP ss8377810 Apr 21, 2003 (117)
3 BUSHMAN ss203946696 Jul 04, 2010 (132)
4 GMI ss283446412 May 04, 2012 (137)
5 1000GENOMES ss1365495333 Aug 21, 2014 (142)
6 ILLUMINA ss1959934117 Feb 12, 2016 (147)
7 ILLUMINA ss2094920233 Dec 20, 2016 (150)
8 USC_VALOUEV ss2158568948 Dec 20, 2016 (150)
9 GRF ss2704266504 Nov 08, 2017 (151)
10 GNOMAD ss2969444830 Nov 08, 2017 (151)
11 ILLUMINA ss3022138747 Nov 08, 2017 (151)
12 BIOINF_KMB_FNS_UNIBA ss3645655179 Oct 12, 2018 (152)
13 URBANLAB ss3651056184 Oct 12, 2018 (152)
14 ILLUMINA ss3652596789 Oct 12, 2018 (152)
15 ACPOP ss3743553791 Jul 13, 2019 (153)
16 KHV_HUMAN_GENOMES ss3822024717 Jul 13, 2019 (153)
17 SGDP_PRJ ss3889490856 Apr 27, 2020 (154)
18 KRGDB ss3939818378 Apr 27, 2020 (154)
19 KOGIC ss3982645747 Apr 27, 2020 (154)
20 TOMMO_GENOMICS ss5230475700 Apr 27, 2021 (155)
21 1000G_HIGH_COVERAGE ss5309442928 Oct 16, 2022 (156)
22 EVA ss5438583832 Oct 16, 2022 (156)
23 TOMMO_GENOMICS ss5790542142 Oct 16, 2022 (156)
24 EVA ss5924166991 Oct 16, 2022 (156)
25 1000Genomes NC_000020.10 - 62263548 Oct 12, 2018 (152)
26 gnomAD - Genomes NC_000020.11 - 63632195 Apr 27, 2021 (155)
27 KOREAN population from KRGDB NC_000020.10 - 62263548 Apr 27, 2020 (154)
28 Korean Genome Project NC_000020.11 - 63632195 Apr 27, 2020 (154)
29 Northern Sweden NC_000020.10 - 62263548 Jul 13, 2019 (153)
30 SGDP_PRJ NC_000020.10 - 62263548 Apr 27, 2020 (154)
31 Siberian NC_000020.10 - 62263548 Apr 27, 2020 (154)
32 8.3KJPN NC_000020.10 - 62263548 Apr 27, 2021 (155)
33 14KJPN NC_000020.11 - 63632195 Oct 16, 2022 (156)
34 ALFA NC_000020.11 - 63632195 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).

Associated ID History Updated (Build)
rs6062291 Aug 27, 2003 (117)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss203946696, ss283446412, ss2094920233 NC_000020.9:61733991:C:A NC_000020.11:63632194:C:A (self)
78983661, 46995772, 16838656, 41507836, 11085302, 88445007, ss1365495333, ss1959934117, ss2158568948, ss2704266504, ss2969444830, ss3022138747, ss3652596789, ss3743553791, ss3889490856, ss3939818378, ss5230475700, ss5438583832 NC_000020.10:62263547:C:A NC_000020.11:63632194:C:A (self)
557003280, 39023748, 124379246, 1057609246, ss3645655179, ss3651056184, ss3822024717, ss3982645747, ss5309442928, ss5790542142, ss5924166991 NC_000020.11:63632194:C:A NC_000020.11:63632194:C:A (self)
ss6638098, ss8377810 NT_011333.5:1000177:C:A NC_000020.11:63632194:C: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 rs4809316

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.post761+d5e8e07