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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.

rs2688069

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:49200495 (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 / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.366376 (96976/264690, TOPMED)
A=0.349497 (48868/139824, GnomAD)
C=0.30076 (8499/28258, 14KJPN) (+ 15 more)
A=0.33790 (6383/18890, ALFA)
C=0.29797 (4994/16760, 8.3KJPN)
A=0.4739 (3035/6404, 1000G_30x)
A=0.4762 (2385/5008, 1000G)
A=0.3236 (1247/3854, ALSPAC)
A=0.3255 (1207/3708, TWINSUK)
C=0.2635 (772/2930, KOREAN)
C=0.2631 (482/1832, Korea1K)
A=0.343 (342/998, GoNL)
A=0.373 (224/600, NorthernSweden)
C=0.285 (118/414, SGDP_PRJ)
A=0.435 (94/216, Qatari)
C=0.274 (58/212, Vietnamese)
A=0.35 (14/40, GENOME_DK)
C=0.32 (12/38, 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 18890 C=0.66210 A=0.33790
European Sub 14286 C=0.67598 A=0.32402
African Sub 2946 C=0.6830 A=0.3170
African Others Sub 114 C=0.649 A=0.351
African American Sub 2832 C=0.6843 A=0.3157
Asian Sub 112 C=0.277 A=0.723
East Asian Sub 86 C=0.29 A=0.71
Other Asian Sub 26 C=0.23 A=0.77
Latin American 1 Sub 146 C=0.610 A=0.390
Latin American 2 Sub 610 C=0.384 A=0.616
South Asian Sub 98 C=0.49 A=0.51
Other Sub 692 C=0.630 A=0.370


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 C=0.633624 A=0.366376
gnomAD - Genomes Global Study-wide 139824 C=0.650503 A=0.349497
gnomAD - Genomes European Sub 75744 C=0.67335 A=0.32665
gnomAD - Genomes African Sub 41858 C=0.68386 A=0.31614
gnomAD - Genomes American Sub 13634 C=0.49817 A=0.50183
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.7089 A=0.2911
gnomAD - Genomes East Asian Sub 3126 C=0.2863 A=0.7137
gnomAD - Genomes Other Sub 2144 C=0.6017 A=0.3983
14KJPN JAPANESE Study-wide 28258 C=0.30076 A=0.69924
Allele Frequency Aggregator Total Global 18890 C=0.66210 A=0.33790
Allele Frequency Aggregator European Sub 14286 C=0.67598 A=0.32402
Allele Frequency Aggregator African Sub 2946 C=0.6830 A=0.3170
Allele Frequency Aggregator Other Sub 692 C=0.630 A=0.370
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.384 A=0.616
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.610 A=0.390
Allele Frequency Aggregator Asian Sub 112 C=0.277 A=0.723
Allele Frequency Aggregator South Asian Sub 98 C=0.49 A=0.51
8.3KJPN JAPANESE Study-wide 16760 C=0.29797 A=0.70203
1000Genomes_30x Global Study-wide 6404 C=0.5261 A=0.4739
1000Genomes_30x African Sub 1786 C=0.6865 A=0.3135
1000Genomes_30x Europe Sub 1266 C=0.6588 A=0.3412
1000Genomes_30x South Asian Sub 1202 C=0.4667 A=0.5333
1000Genomes_30x East Asian Sub 1170 C=0.3009 A=0.6991
1000Genomes_30x American Sub 980 C=0.404 A=0.596
1000Genomes Global Study-wide 5008 C=0.5238 A=0.4762
1000Genomes African Sub 1322 C=0.6891 A=0.3109
1000Genomes East Asian Sub 1008 C=0.3065 A=0.6935
1000Genomes Europe Sub 1006 C=0.6491 A=0.3509
1000Genomes South Asian Sub 978 C=0.467 A=0.533
1000Genomes American Sub 694 C=0.422 A=0.578
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6764 A=0.3236
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6745 A=0.3255
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2635 A=0.7365, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 C=0.2631 A=0.7369
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.657 A=0.343
Northern Sweden ACPOP Study-wide 600 C=0.627 A=0.373
SGDP_PRJ Global Study-wide 414 C=0.285 A=0.715
Qatari Global Study-wide 216 C=0.565 A=0.435
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.274 A=0.726
The Danish reference pan genome Danish Study-wide 40 C=0.65 A=0.35
Siberian Global Study-wide 38 C=0.32 A=0.68
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 22 NC_000022.11:g.49200495C>A
GRCh38.p14 chr 22 NC_000022.11:g.49200495C>G
GRCh37.p13 chr 22 NC_000022.10:g.49596421C>A
GRCh37.p13 chr 22 NC_000022.10:g.49596421C>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
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 G
GRCh38.p14 chr 22 NC_000022.11:g.49200495= NC_000022.11:g.49200495C>A NC_000022.11:g.49200495C>G
GRCh37.p13 chr 22 NC_000022.10:g.49596421= NC_000022.10:g.49596421C>A NC_000022.10:g.49596421C>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#.

62 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3795423 Sep 28, 2001 (100)
2 SC_SNP ss8024488 Apr 21, 2003 (117)
3 SSAHASNP ss21837496 Apr 05, 2004 (121)
4 ABI ss44296469 Mar 14, 2006 (126)
5 HGSV ss78679481 Dec 06, 2007 (129)
6 HGSV ss81754882 Dec 15, 2007 (130)
7 HGSV ss84650187 Dec 15, 2007 (130)
8 HUMANGENOME_JCVI ss96107163 Feb 06, 2009 (130)
9 ILLUMINA-UK ss117443478 Feb 14, 2009 (130)
10 ENSEMBL ss143970293 Dec 01, 2009 (131)
11 GMI ss157296540 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss169581237 Jul 04, 2010 (132)
13 1000GENOMES ss228737079 Jul 14, 2010 (132)
14 1000GENOMES ss238109092 Jul 15, 2010 (132)
15 1000GENOMES ss244218377 Jul 15, 2010 (132)
16 GMI ss283673513 May 04, 2012 (137)
17 GMI ss287586687 Apr 25, 2013 (138)
18 PJP ss292728559 May 09, 2011 (134)
19 SSMP ss662641441 Apr 25, 2013 (138)
20 EVA-GONL ss995461634 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1082736407 Aug 21, 2014 (142)
22 1000GENOMES ss1367586888 Aug 21, 2014 (142)
23 DDI ss1429290951 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1579794085 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1640214755 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1683208788 Apr 01, 2015 (144)
27 HAMMER_LAB ss1809873977 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1939034338 Feb 12, 2016 (147)
29 JJLAB ss2030289575 Sep 14, 2016 (149)
30 USC_VALOUEV ss2158914477 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2248184072 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2629641425 Nov 08, 2017 (151)
33 GRF ss2704668097 Nov 08, 2017 (151)
34 GNOMAD ss2975574825 Nov 08, 2017 (151)
35 SWEGEN ss3019478632 Nov 08, 2017 (151)
36 CSHL ss3352889159 Nov 08, 2017 (151)
37 URBANLAB ss3651201343 Oct 12, 2018 (152)
38 EVA_DECODE ss3708414342 Jul 13, 2019 (153)
39 ACPOP ss3744027098 Jul 13, 2019 (153)
40 EVA ss3759517380 Jul 13, 2019 (153)
41 PACBIO ss3788855309 Jul 13, 2019 (153)
42 PACBIO ss3793716922 Jul 13, 2019 (153)
43 PACBIO ss3798603446 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3822673484 Jul 13, 2019 (153)
45 EVA ss3836046692 Apr 27, 2020 (154)
46 EVA ss3841651627 Apr 27, 2020 (154)
47 EVA ss3847167152 Apr 27, 2020 (154)
48 SGDP_PRJ ss3890780588 Apr 27, 2020 (154)
49 KRGDB ss3941188588 Apr 27, 2020 (154)
50 KOGIC ss3983867622 Apr 27, 2020 (154)
51 TOPMED ss5112810172 Apr 26, 2021 (155)
52 TOMMO_GENOMICS ss5233127364 Apr 26, 2021 (155)
53 1000G_HIGH_COVERAGE ss5311480599 Oct 16, 2022 (156)
54 EVA ss5441994897 Oct 16, 2022 (156)
55 1000G_HIGH_COVERAGE ss5619203833 Oct 16, 2022 (156)
56 SANFORD_IMAGENETICS ss5664705556 Oct 16, 2022 (156)
57 TOMMO_GENOMICS ss5794409489 Oct 16, 2022 (156)
58 YY_MCH ss5818804180 Oct 16, 2022 (156)
59 EVA ss5822221688 Oct 16, 2022 (156)
60 EVA ss5853438014 Oct 16, 2022 (156)
61 EVA ss5882247144 Oct 16, 2022 (156)
62 EVA ss5959565162 Oct 16, 2022 (156)
63 1000Genomes NC_000022.10 - 49596421 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000022.11 - 49200495 Oct 16, 2022 (156)
65 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 49596421 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000022.10 - 49596421 Apr 27, 2020 (154)
67 gnomAD - Genomes NC_000022.11 - 49200495 Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000022.10 - 49596421 Apr 27, 2020 (154)
69 KOREAN population from KRGDB NC_000022.10 - 49596421 Apr 27, 2020 (154)
70 Korean Genome Project NC_000022.11 - 49200495 Apr 27, 2020 (154)
71 Northern Sweden NC_000022.10 - 49596421 Jul 13, 2019 (153)
72 Qatari NC_000022.10 - 49596421 Apr 27, 2020 (154)
73 SGDP_PRJ NC_000022.10 - 49596421 Apr 27, 2020 (154)
74 Siberian NC_000022.10 - 49596421 Apr 27, 2020 (154)
75 8.3KJPN NC_000022.10 - 49596421 Apr 26, 2021 (155)
76 14KJPN NC_000022.11 - 49200495 Oct 16, 2022 (156)
77 TopMed NC_000022.11 - 49200495 Apr 26, 2021 (155)
78 UK 10K study - Twins NC_000022.10 - 49596421 Oct 12, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000022.10 - 49596421 Jul 13, 2019 (153)
80 ALFA NC_000022.11 - 49200495 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)
rs5770020 Aug 27, 2003 (117)
rs60119623 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78679481, ss81754882, ss84650187 NC_000022.8:47917281:C:A NC_000022.11:49200494:C:A (self)
ss117443478, ss169581237, ss283673513, ss287586687, ss292728559 NC_000022.9:47982424:C:A NC_000022.11:49200494:C:A (self)
81153861, 44891230, 5959024, 20000407, 48365982, 17311963, 21076260, 42797568, 11430831, 91096671, 44891230, 9898843, ss228737079, ss238109092, ss244218377, ss662641441, ss995461634, ss1082736407, ss1367586888, ss1429290951, ss1579794085, ss1640214755, ss1683208788, ss1809873977, ss1939034338, ss2030289575, ss2158914477, ss2629641425, ss2704668097, ss2975574825, ss3019478632, ss3352889159, ss3744027098, ss3759517380, ss3788855309, ss3793716922, ss3798603446, ss3836046692, ss3841651627, ss3890780588, ss3941188588, ss5233127364, ss5441994897, ss5664705556, ss5822221688, ss5959565162 NC_000022.10:49596420:C:A NC_000022.11:49200494:C:A (self)
106729768, 572971360, 40245623, 128246593, 387919119, 6071625135, ss2248184072, ss3651201343, ss3708414342, ss3822673484, ss3847167152, ss3983867622, ss5112810172, ss5311480599, ss5619203833, ss5794409489, ss5818804180, ss5853438014, ss5882247144 NC_000022.11:49200494:C:A NC_000022.11:49200494:C:A (self)
ss3795423, ss8024488, ss44296469, ss96107163, ss143970293, ss157296540 NT_011520.12:28986989:C:A NC_000022.11:49200494:C:A (self)
ss21837496 NT_011525.5:302813:C:A NC_000022.11:49200494:C:A (self)
48365982, ss3941188588 NC_000022.10:49596420:C:G NC_000022.11:49200494:C: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 rs2688069

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