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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.

rs9680615

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:19783363 (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=0.114032 (30183/264690, TOPMED)
A=0.125004 (17509/140068, GnomAD)
A=0.07548 (5940/78698, PAGE_STUDY) (+ 17 more)
A=0.15622 (5844/37408, ALFA)
A=0.01525 (431/28258, 14KJPN)
A=0.01492 (250/16760, 8.3KJPN)
A=0.0796 (510/6404, 1000G_30x)
A=0.0765 (383/5008, 1000G)
A=0.1804 (808/4480, Estonian)
A=0.1798 (693/3854, ALSPAC)
A=0.1702 (631/3708, TWINSUK)
A=0.0270 (79/2922, KOREAN)
A=0.0284 (52/1832, Korea1K)
A=0.159 (159/998, GoNL)
A=0.143 (86/600, NorthernSweden)
A=0.037 (8/216, Qatari)
A=0.088 (19/216, Vietnamese)
G=0.46 (25/54, SGDP_PRJ)
A=0.20 (8/40, GENOME_DK)
G=0.4 (3/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TBX1 : 3 Prime UTR Variant
GNB1L : 3 Prime UTR 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 37502 G=0.84403 A=0.15597
European Sub 31010 G=0.83015 A=0.16985
African Sub 3176 G=0.9279 A=0.0721
African Others Sub 124 G=0.952 A=0.048
African American Sub 3052 G=0.9269 A=0.0731
Asian Sub 162 G=0.957 A=0.043
East Asian Sub 134 G=0.963 A=0.037
Other Asian Sub 28 G=0.93 A=0.07
Latin American 1 Sub 168 G=0.935 A=0.065
Latin American 2 Sub 700 G=0.903 A=0.097
South Asian Sub 120 G=0.942 A=0.058
Other Sub 2166 G=0.8800 A=0.1200


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=0.885968 A=0.114032
gnomAD - Genomes Global Study-wide 140068 G=0.874996 A=0.125004
gnomAD - Genomes European Sub 75844 G=0.83423 A=0.16577
gnomAD - Genomes African Sub 41978 G=0.93101 A=0.06899
gnomAD - Genomes American Sub 13646 G=0.89821 A=0.10179
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9061 A=0.0939
gnomAD - Genomes East Asian Sub 3130 G=0.9665 A=0.0335
gnomAD - Genomes Other Sub 2148 G=0.8911 A=0.1089
The PAGE Study Global Study-wide 78698 G=0.92452 A=0.07548
The PAGE Study AfricanAmerican Sub 32514 G=0.92446 A=0.07554
The PAGE Study Mexican Sub 10810 G=0.91082 A=0.08918
The PAGE Study Asian Sub 8316 G=0.9802 A=0.0198
The PAGE Study PuertoRican Sub 7918 G=0.9067 A=0.0933
The PAGE Study NativeHawaiian Sub 4534 G=0.9497 A=0.0503
The PAGE Study Cuban Sub 4230 G=0.8863 A=0.1137
The PAGE Study Dominican Sub 3828 G=0.9167 A=0.0833
The PAGE Study CentralAmerican Sub 2450 G=0.9233 A=0.0767
The PAGE Study SouthAmerican Sub 1982 G=0.9057 A=0.0943
The PAGE Study NativeAmerican Sub 1260 G=0.8675 A=0.1325
The PAGE Study SouthAsian Sub 856 G=0.946 A=0.054
Allele Frequency Aggregator Total Global 37408 G=0.84378 A=0.15622
Allele Frequency Aggregator European Sub 30934 G=0.82983 A=0.17017
Allele Frequency Aggregator African Sub 3176 G=0.9279 A=0.0721
Allele Frequency Aggregator Other Sub 2148 G=0.8799 A=0.1201
Allele Frequency Aggregator Latin American 2 Sub 700 G=0.903 A=0.097
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.935 A=0.065
Allele Frequency Aggregator Asian Sub 162 G=0.957 A=0.043
Allele Frequency Aggregator South Asian Sub 120 G=0.942 A=0.058
14KJPN JAPANESE Study-wide 28258 G=0.98475 A=0.01525
8.3KJPN JAPANESE Study-wide 16760 G=0.98508 A=0.01492
1000Genomes_30x Global Study-wide 6404 G=0.9204 A=0.0796
1000Genomes_30x African Sub 1786 G=0.9558 A=0.0442
1000Genomes_30x Europe Sub 1266 G=0.8191 A=0.1809
1000Genomes_30x South Asian Sub 1202 G=0.9509 A=0.0491
1000Genomes_30x East Asian Sub 1170 G=0.9453 A=0.0547
1000Genomes_30x American Sub 980 G=0.919 A=0.081
1000Genomes Global Study-wide 5008 G=0.9235 A=0.0765
1000Genomes African Sub 1322 G=0.9584 A=0.0416
1000Genomes East Asian Sub 1008 G=0.9514 A=0.0486
1000Genomes Europe Sub 1006 G=0.8241 A=0.1759
1000Genomes South Asian Sub 978 G=0.953 A=0.047
1000Genomes American Sub 694 G=0.919 A=0.081
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8196 A=0.1804
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8202 A=0.1798
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8298 A=0.1702
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9730 A=0.0270
Korean Genome Project KOREAN Study-wide 1832 G=0.9716 A=0.0284
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.841 A=0.159
Northern Sweden ACPOP Study-wide 600 G=0.857 A=0.143
Qatari Global Study-wide 216 G=0.963 A=0.037
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.912 A=0.088
SGDP_PRJ Global Study-wide 54 G=0.46 A=0.54
The Danish reference pan genome Danish Study-wide 40 G=0.80 A=0.20
Siberian Global Study-wide 8 G=0.4 A=0.6
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.19783363G>A
GRCh37.p13 chr 22 NC_000022.10:g.19770886G>A
TBX1 RefSeqGene (LRG_226) NG_009229.1:g.31661G>A
Gene: TBX1, T-box transcription factor 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TBX1 transcript variant B NM_005992.1:c.*60= N/A 3 Prime UTR Variant
TBX1 transcript variant D NM_001379200.1:c. N/A Genic Downstream Transcript Variant
TBX1 transcript variant A NM_080646.2:c. N/A Genic Downstream Transcript Variant
TBX1 transcript variant C NM_080647.1:c. N/A Genic Downstream Transcript Variant
TBX1 transcript variant X2 XM_006724312.3:c. N/A Genic Downstream Transcript Variant
TBX1 transcript variant X3 XM_017028926.2:c. N/A Genic Downstream Transcript Variant
TBX1 transcript variant X1 XM_017028927.2:c. N/A Genic Downstream Transcript Variant
Gene: GNB1L, G protein subunit beta 1 like (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GNB1L transcript NM_053004.3:c.*5346= N/A 3 Prime UTR 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 22 NC_000022.11:g.19783363= NC_000022.11:g.19783363G>A
GRCh37.p13 chr 22 NC_000022.10:g.19770886= NC_000022.10:g.19770886G>A
TBX1 RefSeqGene (LRG_226) NG_009229.1:g.31661= NG_009229.1:g.31661G>A
TBX1 transcript variant B NM_005992.1:c.*60= NM_005992.1:c.*60G>A
GNB1L transcript NM_053004.3:c.*5346= NM_053004.3:c.*5346C>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#.

77 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13479442 Dec 05, 2003 (119)
2 ABI ss41521870 Mar 14, 2006 (126)
3 EGP_SNPS ss52470901 Oct 16, 2006 (127)
4 HGSV ss81126329 Dec 15, 2007 (130)
5 BCMHGSC_JDW ss91877193 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss96114763 Feb 06, 2009 (130)
7 ILLUMINA-UK ss117361549 Feb 14, 2009 (130)
8 ENSEMBL ss138335020 Dec 01, 2009 (131)
9 ENSEMBL ss143751569 Dec 01, 2009 (131)
10 1000GENOMES ss212101927 Jul 14, 2010 (132)
11 1000GENOMES ss228617251 Jul 14, 2010 (132)
12 1000GENOMES ss238021738 Jul 15, 2010 (132)
13 1000GENOMES ss244151259 Jul 15, 2010 (132)
14 BL ss255842024 May 09, 2011 (134)
15 GMI ss283586650 May 04, 2012 (137)
16 PJP ss292736010 May 09, 2011 (134)
17 ILLUMINA ss483594299 May 04, 2012 (137)
18 ILLUMINA ss484288992 May 04, 2012 (137)
19 ILLUMINA ss535799584 Sep 08, 2015 (146)
20 SSMP ss662482721 Apr 25, 2013 (138)
21 ILLUMINA ss779511369 Sep 08, 2015 (146)
22 ILLUMINA ss782240578 Sep 08, 2015 (146)
23 ILLUMINA ss834981733 Sep 08, 2015 (146)
24 EVA-GONL ss995221198 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1082569407 Aug 21, 2014 (142)
26 1000GENOMES ss1366677229 Aug 21, 2014 (142)
27 DDI ss1429219431 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1579703675 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1639750907 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1682744940 Apr 01, 2015 (144)
31 EVA_DECODE ss1699290366 Apr 01, 2015 (144)
32 WEILL_CORNELL_DGM ss1938782704 Feb 12, 2016 (147)
33 ILLUMINA ss1959965476 Feb 12, 2016 (147)
34 GENOMED ss1969246677 Jul 19, 2016 (147)
35 JJLAB ss2030164393 Sep 14, 2016 (149)
36 USC_VALOUEV ss2158774193 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2246444997 Dec 20, 2016 (150)
38 ILLUMINA ss2633862534 Nov 08, 2017 (151)
39 GRF ss2704517119 Nov 08, 2017 (151)
40 GNOMAD ss2972970031 Nov 08, 2017 (151)
41 AFFY ss2985233184 Nov 08, 2017 (151)
42 AFFY ss2985850530 Nov 08, 2017 (151)
43 SWEGEN ss3019083625 Nov 08, 2017 (151)
44 ILLUMINA ss3022171654 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3028919871 Nov 08, 2017 (151)
46 CSHL ss3352775675 Nov 08, 2017 (151)
47 ILLUMINA ss3628505603 Oct 12, 2018 (152)
48 ILLUMINA ss3631814957 Oct 12, 2018 (152)
49 URBANLAB ss3651151515 Oct 12, 2018 (152)
50 ILLUMINA ss3652633202 Oct 12, 2018 (152)
51 ILLUMINA ss3654001237 Oct 12, 2018 (152)
52 EGCUT_WGS ss3685616333 Jul 13, 2019 (153)
53 EVA_DECODE ss3707952044 Jul 13, 2019 (153)
54 ILLUMINA ss3725957327 Jul 13, 2019 (153)
55 ACPOP ss3743821950 Jul 13, 2019 (153)
56 EVA ss3759228924 Jul 13, 2019 (153)
57 PAGE_CC ss3772082130 Jul 13, 2019 (153)
58 KHV_HUMAN_GENOMES ss3822396988 Jul 13, 2019 (153)
59 EVA ss3825965378 Apr 27, 2020 (154)
60 EVA ss3835926988 Apr 27, 2020 (154)
61 SGDP_PRJ ss3890253754 Apr 27, 2020 (154)
62 KRGDB ss3940636623 Apr 27, 2020 (154)
63 KOGIC ss3983386263 Apr 27, 2020 (154)
64 TOPMED ss5105060339 Apr 26, 2021 (155)
65 TOMMO_GENOMICS ss5232033958 Apr 26, 2021 (155)
66 1000G_HIGH_COVERAGE ss5310653047 Oct 16, 2022 (156)
67 EVA ss5316046846 Oct 16, 2022 (156)
68 EVA ss5440515454 Oct 16, 2022 (156)
69 HUGCELL_USP ss5502564599 Oct 16, 2022 (156)
70 1000G_HIGH_COVERAGE ss5618009542 Oct 16, 2022 (156)
71 SANFORD_IMAGENETICS ss5664233690 Oct 16, 2022 (156)
72 TOMMO_GENOMICS ss5792982635 Oct 16, 2022 (156)
73 YY_MCH ss5818594495 Oct 16, 2022 (156)
74 EVA ss5821898036 Oct 16, 2022 (156)
75 EVA ss5853345781 Oct 16, 2022 (156)
76 EVA ss5881342634 Oct 16, 2022 (156)
77 EVA ss5959105086 Oct 16, 2022 (156)
78 1000Genomes NC_000022.10 - 19770886 Oct 12, 2018 (152)
79 1000Genomes_30x NC_000022.11 - 19783363 Oct 16, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 19770886 Oct 12, 2018 (152)
81 Genetic variation in the Estonian population NC_000022.10 - 19770886 Oct 12, 2018 (152)
82 The Danish reference pan genome NC_000022.10 - 19770886 Apr 27, 2020 (154)
83 gnomAD - Genomes NC_000022.11 - 19783363 Apr 26, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000022.10 - 19770886 Apr 27, 2020 (154)
85 KOREAN population from KRGDB NC_000022.10 - 19770886 Apr 27, 2020 (154)
86 Korean Genome Project NC_000022.11 - 19783363 Apr 27, 2020 (154)
87 Northern Sweden NC_000022.10 - 19770886 Jul 13, 2019 (153)
88 The PAGE Study NC_000022.11 - 19783363 Jul 13, 2019 (153)
89 Qatari NC_000022.10 - 19770886 Apr 27, 2020 (154)
90 SGDP_PRJ NC_000022.10 - 19770886 Apr 27, 2020 (154)
91 Siberian NC_000022.10 - 19770886 Apr 27, 2020 (154)
92 8.3KJPN NC_000022.10 - 19770886 Apr 26, 2021 (155)
93 14KJPN NC_000022.11 - 19783363 Oct 16, 2022 (156)
94 TopMed NC_000022.11 - 19783363 Apr 26, 2021 (155)
95 UK 10K study - Twins NC_000022.10 - 19770886 Oct 12, 2018 (152)
96 A Vietnamese Genetic Variation Database NC_000022.10 - 19770886 Jul 13, 2019 (153)
97 ALFA NC_000022.11 - 19783363 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)
rs60917166 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81126329 NC_000022.8:18145439:G:A NC_000022.11:19783362:G:A (self)
ss91877193, ss117361549, ss212101927, ss255842024, ss283586650, ss292736010, ss484288992, ss1699290366 NC_000022.9:18150885:G:A NC_000022.11:19783362:G:A (self)
80211481, 44378725, 31354581, 5868614, 19772375, 47814017, 17106815, 20824626, 42270734, 11290547, 90003265, 44378725, 9791780, ss228617251, ss238021738, ss244151259, ss483594299, ss535799584, ss662482721, ss779511369, ss782240578, ss834981733, ss995221198, ss1082569407, ss1366677229, ss1429219431, ss1579703675, ss1639750907, ss1682744940, ss1938782704, ss1959965476, ss1969246677, ss2030164393, ss2158774193, ss2633862534, ss2704517119, ss2972970031, ss2985233184, ss2985850530, ss3019083625, ss3022171654, ss3352775675, ss3628505603, ss3631814957, ss3652633202, ss3654001237, ss3685616333, ss3743821950, ss3759228924, ss3825965378, ss3835926988, ss3890253754, ss3940636623, ss5232033958, ss5316046846, ss5440515454, ss5664233690, ss5821898036, ss5959105086 NC_000022.10:19770885:G:A NC_000022.11:19783362:G:A (self)
105535477, 566504348, 39764264, 1303599, 126819739, 380169286, 10756348293, ss2246444997, ss3028919871, ss3651151515, ss3707952044, ss3725957327, ss3772082130, ss3822396988, ss3983386263, ss5105060339, ss5310653047, ss5502564599, ss5618009542, ss5792982635, ss5818594495, ss5853345781, ss5881342634 NC_000022.11:19783362:G:A NC_000022.11:19783362:G:A (self)
ss13479442, ss41521870, ss52470901, ss96114763, ss138335020, ss143751569 NT_011519.10:2923035:G:A NC_000022.11:19783362: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 rs9680615

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