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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.

rs7101429

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:78281921 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.155280 (41101/264690, TOPMED)
G=0.146546 (20541/140168, GnomAD)
G=0.16644 (4738/28466, ALFA) (+ 20 more)
G=0.44324 (12525/28258, 14KJPN)
G=0.44814 (7510/16758, 8.3KJPN)
G=0.2227 (1426/6404, 1000G_30x)
G=0.2306 (1155/5008, 1000G)
G=0.1674 (750/4480, Estonian)
G=0.1500 (578/3854, ALSPAC)
G=0.1510 (560/3708, TWINSUK)
G=0.3990 (1169/2930, KOREAN)
G=0.2153 (407/1890, HapMap)
G=0.3826 (701/1832, Korea1K)
G=0.2677 (303/1132, Daghestan)
G=0.138 (138/998, GoNL)
G=0.397 (311/784, PRJEB37584)
G=0.331 (207/626, Chileans)
G=0.257 (154/600, NorthernSweden)
A=0.430 (110/256, SGDP_PRJ)
G=0.287 (62/216, Qatari)
G=0.343 (74/216, Vietnamese)
G=0.25 (10/40, GENOME_DK)
A=0.43 (12/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GAB2 : Intron Variant
Publications
10 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 28466 A=0.83356 G=0.16644
European Sub 17478 A=0.82715 G=0.17285
African Sub 6256 A=0.9329 G=0.0671
African Others Sub 210 A=0.971 G=0.029
African American Sub 6046 A=0.9315 G=0.0685
Asian Sub 162 A=0.660 G=0.340
East Asian Sub 104 A=0.587 G=0.413
Other Asian Sub 58 A=0.79 G=0.21
Latin American 1 Sub 290 A=0.821 G=0.179
Latin American 2 Sub 2760 A=0.6957 G=0.3043
South Asian Sub 112 A=0.688 G=0.312
Other Sub 1408 A=0.7763 G=0.2237


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 A=0.844720 G=0.155280
gnomAD - Genomes Global Study-wide 140168 A=0.853454 G=0.146546
gnomAD - Genomes European Sub 75898 A=0.83466 G=0.16534
gnomAD - Genomes African Sub 42026 A=0.93956 G=0.06044
gnomAD - Genomes American Sub 13640 A=0.76503 G=0.23497
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8084 G=0.1916
gnomAD - Genomes East Asian Sub 3126 A=0.6011 G=0.3989
gnomAD - Genomes Other Sub 2154 A=0.8315 G=0.1685
Allele Frequency Aggregator Total Global 28466 A=0.83356 G=0.16644
Allele Frequency Aggregator European Sub 17478 A=0.82715 G=0.17285
Allele Frequency Aggregator African Sub 6256 A=0.9329 G=0.0671
Allele Frequency Aggregator Latin American 2 Sub 2760 A=0.6957 G=0.3043
Allele Frequency Aggregator Other Sub 1408 A=0.7763 G=0.2237
Allele Frequency Aggregator Latin American 1 Sub 290 A=0.821 G=0.179
Allele Frequency Aggregator Asian Sub 162 A=0.660 G=0.340
Allele Frequency Aggregator South Asian Sub 112 A=0.688 G=0.312
14KJPN JAPANESE Study-wide 28258 A=0.55676 G=0.44324
8.3KJPN JAPANESE Study-wide 16758 A=0.55186 G=0.44814
1000Genomes_30x Global Study-wide 6404 A=0.7773 G=0.2227
1000Genomes_30x African Sub 1786 A=0.9451 G=0.0549
1000Genomes_30x Europe Sub 1266 A=0.8389 G=0.1611
1000Genomes_30x South Asian Sub 1202 A=0.7072 G=0.2928
1000Genomes_30x East Asian Sub 1170 A=0.5974 G=0.4026
1000Genomes_30x American Sub 980 A=0.693 G=0.307
1000Genomes Global Study-wide 5008 A=0.7694 G=0.2306
1000Genomes African Sub 1322 A=0.9433 G=0.0567
1000Genomes East Asian Sub 1008 A=0.5972 G=0.4028
1000Genomes Europe Sub 1006 A=0.8250 G=0.1750
1000Genomes South Asian Sub 978 A=0.708 G=0.292
1000Genomes American Sub 694 A=0.695 G=0.305
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8326 G=0.1674
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8500 G=0.1500
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8490 G=0.1510
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6010 C=0.0000, G=0.3990
HapMap Global Study-wide 1890 A=0.7847 G=0.2153
HapMap American Sub 768 A=0.749 G=0.251
HapMap African Sub 692 A=0.909 G=0.091
HapMap Asian Sub 254 A=0.563 G=0.437
HapMap Europe Sub 176 A=0.773 G=0.227
Korean Genome Project KOREAN Study-wide 1832 A=0.6174 G=0.3826
Genome-wide autozygosity in Daghestan Global Study-wide 1132 A=0.7323 G=0.2677
Genome-wide autozygosity in Daghestan Daghestan Sub 626 A=0.735 G=0.265
Genome-wide autozygosity in Daghestan Near_East Sub 142 A=0.761 G=0.239
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.680 G=0.320
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.852 G=0.148
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.65 G=0.35
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.61 G=0.39
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.862 G=0.138
CNV burdens in cranial meningiomas Global Study-wide 784 A=0.603 G=0.397
CNV burdens in cranial meningiomas CRM Sub 784 A=0.603 G=0.397
Chileans Chilean Study-wide 626 A=0.669 G=0.331
Northern Sweden ACPOP Study-wide 600 A=0.743 G=0.257
SGDP_PRJ Global Study-wide 256 A=0.430 G=0.570
Qatari Global Study-wide 216 A=0.713 G=0.287
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.657 G=0.343
The Danish reference pan genome Danish Study-wide 40 A=0.75 G=0.25
Siberian Global Study-wide 28 A=0.43 G=0.57
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 11 NC_000011.10:g.78281921A>C
GRCh38.p14 chr 11 NC_000011.10:g.78281921A>G
GRCh37.p13 chr 11 NC_000011.9:g.77992967A>C
GRCh37.p13 chr 11 NC_000011.9:g.77992967A>G
GAB2 RefSeqGene NG_016171.1:g.140902T>G
GAB2 RefSeqGene NG_016171.1:g.140902T>C
Gene: GAB2, GRB2 associated binding protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GAB2 transcript variant 2 NM_012296.4:c.-39-1020T>G N/A Intron Variant
GAB2 transcript variant 1 NM_080491.3:c.76-1020T>G N/A Intron Variant
GAB2 transcript variant X1 XM_024448782.2:c.22-1020T…

XM_024448782.2:c.22-1020T>G

N/A Intron Variant
GAB2 transcript variant X2 XM_047427935.1:c.-39-1020…

XM_047427935.1:c.-39-1020T>G

N/A Intron Variant
GAB2 transcript variant X3 XM_047427936.1:c.-39-1020…

XM_047427936.1:c.-39-1020T>G

N/A Intron 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 A= C G
GRCh38.p14 chr 11 NC_000011.10:g.78281921= NC_000011.10:g.78281921A>C NC_000011.10:g.78281921A>G
GRCh37.p13 chr 11 NC_000011.9:g.77992967= NC_000011.9:g.77992967A>C NC_000011.9:g.77992967A>G
GAB2 RefSeqGene NG_016171.1:g.140902= NG_016171.1:g.140902T>G NG_016171.1:g.140902T>C
GAB2 transcript variant 2 NM_012296.3:c.-39-1020= NM_012296.3:c.-39-1020T>G NM_012296.3:c.-39-1020T>C
GAB2 transcript variant 2 NM_012296.4:c.-39-1020= NM_012296.4:c.-39-1020T>G NM_012296.4:c.-39-1020T>C
GAB2 transcript variant 1 NM_080491.2:c.76-1020= NM_080491.2:c.76-1020T>G NM_080491.2:c.76-1020T>C
GAB2 transcript variant 1 NM_080491.3:c.76-1020= NM_080491.3:c.76-1020T>G NM_080491.3:c.76-1020T>C
GAB2 transcript variant X1 XM_024448782.2:c.22-1020= XM_024448782.2:c.22-1020T>G XM_024448782.2:c.22-1020T>C
GAB2 transcript variant X2 XM_047427935.1:c.-39-1020= XM_047427935.1:c.-39-1020T>G XM_047427935.1:c.-39-1020T>C
GAB2 transcript variant X3 XM_047427936.1:c.-39-1020= XM_047427936.1:c.-39-1020T>G XM_047427936.1:c.-39-1020T>C
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#.

64 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10645478 Jul 11, 2003 (116)
2 AFFY ss66051895 Nov 30, 2006 (127)
3 AFFY ss75958412 Dec 07, 2007 (129)
4 KRIBB_YJKIM ss82383689 Dec 14, 2007 (130)
5 BGI ss102978515 Dec 01, 2009 (131)
6 1000GENOMES ss110696988 Jan 25, 2009 (130)
7 GMI ss156502477 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss168601460 Jul 04, 2010 (132)
9 AFFY ss169676441 Jul 04, 2010 (132)
10 1000GENOMES ss225328159 Jul 14, 2010 (132)
11 1000GENOMES ss235621469 Jul 15, 2010 (132)
12 1000GENOMES ss242241695 Jul 15, 2010 (132)
13 GMI ss281075554 May 04, 2012 (137)
14 PJP ss291077891 May 09, 2011 (134)
15 ILLUMINA ss410946538 Sep 17, 2011 (135)
16 TISHKOFF ss562669759 Apr 25, 2013 (138)
17 SSMP ss658184081 Apr 25, 2013 (138)
18 EVA-GONL ss988704889 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1077853769 Aug 21, 2014 (142)
20 1000GENOMES ss1341998621 Aug 21, 2014 (142)
21 HAMMER_LAB ss1397609548 Sep 08, 2015 (146)
22 DDI ss1426683651 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1575806510 Apr 01, 2015 (144)
24 EVA_DECODE ss1598366448 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1626953705 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1669947738 Apr 01, 2015 (144)
27 EVA_SVP ss1713266183 Apr 01, 2015 (144)
28 HAMMER_LAB ss1806888847 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1932060692 Feb 12, 2016 (147)
30 GENOMED ss1967396988 Jul 19, 2016 (147)
31 JJLAB ss2026774155 Sep 14, 2016 (149)
32 USC_VALOUEV ss2155086245 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2183772523 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2627861553 Nov 08, 2017 (151)
35 GRF ss2699382570 Nov 08, 2017 (151)
36 GNOMAD ss2901736073 Nov 08, 2017 (151)
37 SWEGEN ss3008391792 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3027184497 Nov 08, 2017 (151)
39 CSHL ss3349679400 Nov 08, 2017 (151)
40 EGCUT_WGS ss3675711538 Jul 13, 2019 (153)
41 EVA_DECODE ss3692138767 Jul 13, 2019 (153)
42 ACPOP ss3738328242 Jul 13, 2019 (153)
43 EVA ss3749515958 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3814850288 Jul 13, 2019 (153)
45 EVA ss3832714375 Apr 26, 2020 (154)
46 SGDP_PRJ ss3876632343 Apr 26, 2020 (154)
47 KRGDB ss3925047304 Apr 26, 2020 (154)
48 KOGIC ss3970297982 Apr 26, 2020 (154)
49 EVA ss3984653450 Apr 26, 2021 (155)
50 TOPMED ss4891536946 Apr 26, 2021 (155)
51 TOMMO_GENOMICS ss5202821861 Apr 26, 2021 (155)
52 1000G_HIGH_COVERAGE ss5288062804 Oct 16, 2022 (156)
53 EVA ss5400720394 Oct 16, 2022 (156)
54 HUGCELL_USP ss5483153706 Oct 16, 2022 (156)
55 EVA ss5510422757 Oct 16, 2022 (156)
56 1000G_HIGH_COVERAGE ss5584098279 Oct 16, 2022 (156)
57 SANFORD_IMAGENETICS ss5624279113 Oct 16, 2022 (156)
58 SANFORD_IMAGENETICS ss5651580710 Oct 16, 2022 (156)
59 TOMMO_GENOMICS ss5750969920 Oct 16, 2022 (156)
60 YY_MCH ss5812570323 Oct 16, 2022 (156)
61 EVA ss5836902158 Oct 16, 2022 (156)
62 EVA ss5850047583 Oct 16, 2022 (156)
63 EVA ss5920694100 Oct 16, 2022 (156)
64 EVA ss5942894791 Oct 16, 2022 (156)
65 1000Genomes NC_000011.9 - 77992967 Oct 12, 2018 (152)
66 1000Genomes_30x NC_000011.10 - 78281921 Oct 16, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 77992967 Oct 12, 2018 (152)
68 Chileans NC_000011.9 - 77992967 Apr 26, 2020 (154)
69 Genome-wide autozygosity in Daghestan NC_000011.8 - 77670615 Apr 26, 2020 (154)
70 Genetic variation in the Estonian population NC_000011.9 - 77992967 Oct 12, 2018 (152)
71 The Danish reference pan genome NC_000011.9 - 77992967 Apr 26, 2020 (154)
72 gnomAD - Genomes NC_000011.10 - 78281921 Apr 26, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000011.9 - 77992967 Apr 26, 2020 (154)
74 HapMap NC_000011.10 - 78281921 Apr 26, 2020 (154)
75 KOREAN population from KRGDB NC_000011.9 - 77992967 Apr 26, 2020 (154)
76 Korean Genome Project NC_000011.10 - 78281921 Apr 26, 2020 (154)
77 Northern Sweden NC_000011.9 - 77992967 Jul 13, 2019 (153)
78 CNV burdens in cranial meningiomas NC_000011.9 - 77992967 Apr 26, 2021 (155)
79 Qatari NC_000011.9 - 77992967 Apr 26, 2020 (154)
80 SGDP_PRJ NC_000011.9 - 77992967 Apr 26, 2020 (154)
81 Siberian NC_000011.9 - 77992967 Apr 26, 2020 (154)
82 8.3KJPN NC_000011.9 - 77992967 Apr 26, 2021 (155)
83 14KJPN NC_000011.10 - 78281921 Oct 16, 2022 (156)
84 TopMed NC_000011.10 - 78281921 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000011.9 - 77992967 Oct 12, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000011.9 - 77992967 Jul 13, 2019 (153)
87 ALFA NC_000011.10 - 78281921 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)
rs57584348 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
32224698, ss3925047304 NC_000011.9:77992966:A:C NC_000011.10:78281920:A:C (self)
80742, ss66051895, ss75958412, ss110696988, ss168601460, ss169676441, ss281075554, ss291077891, ss410946538, ss1397609548, ss1598366448, ss1713266183 NC_000011.8:77670614:A:G NC_000011.10:78281920:A:G (self)
54545796, 30274502, 78702, 21449786, 2633336, 13507564, 32224698, 11613107, 202930, 14102622, 28649323, 7602599, 60791168, 30274502, 6714526, ss225328159, ss235621469, ss242241695, ss562669759, ss658184081, ss988704889, ss1077853769, ss1341998621, ss1426683651, ss1575806510, ss1626953705, ss1669947738, ss1806888847, ss1932060692, ss1967396988, ss2026774155, ss2155086245, ss2627861553, ss2699382570, ss2901736073, ss3008391792, ss3349679400, ss3675711538, ss3738328242, ss3749515958, ss3832714375, ss3876632343, ss3925047304, ss3984653450, ss5202821861, ss5400720394, ss5510422757, ss5624279113, ss5651580710, ss5836902158, ss5942894791 NC_000011.9:77992966:A:G NC_000011.10:78281920:A:G (self)
71624214, 385009798, 642297, 26675983, 84807024, 107082602, 8776613543, ss2183772523, ss3027184497, ss3692138767, ss3814850288, ss3970297982, ss4891536946, ss5288062804, ss5483153706, ss5584098279, ss5750969920, ss5812570323, ss5850047583, ss5920694100 NC_000011.10:78281920:A:G NC_000011.10:78281920:A:G (self)
ss10645478 NT_033927.5:8191995:A:G NC_000011.10:78281920:A:G (self)
ss82383689, ss102978515, ss156502477 NT_167190.1:23298761:A:G NC_000011.10:78281920:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

10 citations for rs7101429
PMID Title Author Year Journal
17553421 GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers. Reiman EM et al. 2007 Neuron
18854865 GAB2 is not associated with late-onset Alzheimer's disease in Japanese. Miyashita A et al. 2009 European journal of human genetics
19204163 GAB2 as an Alzheimer disease susceptibility gene: follow-up of genomewide association results. Schjeide BM et al. 2009 Archives of neurology
20568290 Identifying genetic interactions in genome-wide data using Bayesian networks. Jiang X et al. 2010 Genetic epidemiology
20594621 The genetic architecture of Alzheimer's disease: beyond APP, PSENs and APOE. Guerreiro RJ et al. 2012 Neurobiology of aging
20888920 Association between GAB2 haplotype and higher glucose metabolism in Alzheimer's disease-affected brain regions in cognitively normal APOEε4 carriers. Liang WS et al. 2011 NeuroImage
21132329 Investigation of 15 of the top candidate genes for late-onset Alzheimer's disease. Belbin O et al. 2011 Human genetics
21285854 Association study of the GAB2 gene with the risk of Alzheimer disease in the chinese population. Wang G et al. 2011 Alzheimer disease and associated disorders
21853025 A bayesian method for evaluating and discovering disease loci associations. Jiang X et al. 2011 PloS one
23071633 Mining pure, strict epistatic interactions from high-dimensional datasets: ameliorating the curse of dimensionality. Jiang X et al. 2012 PloS one
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