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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 Aliases 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.

rs2664170

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chrX:154717327 (GRCh38.p12) 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
G=0.37381 (46938/125568, TOPMED)
G=0.3617 (7709/21315, GnomAD)
G=0.353 (1331/3775, 1000G) (+ 3 more)
G=0.329 (1221/3708, TWINSUK)
G=0.333 (963/2889, ALSPAC)
G=0.1 (7/48, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GAB3 : Intron Variant
Publications
7 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.p12 chr X NC_000023.11:g.154717327G>A
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.2151306G>A
GAB3 RefSeqGene NG_012834.2:g.38747C>T
GRCh37.p13 chr X NC_000023.10:g.153945602G>A
Gene: GAB3, GRB2 associated binding protein 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GAB3 transcript variant 1 NM_001081573.3:c. N/A Intron Variant
GAB3 transcript variant 3 NM_001282283.2:c. N/A Intron Variant
GAB3 transcript variant 2 NM_080612.4:c. N/A Intron Variant
GAB3 transcript variant 4 NR_104114.1:n. N/A Intron Variant
GAB3 transcript variant X5 XM_005274648.1:c. N/A Intron Variant
GAB3 transcript variant X4 XM_006724804.1:c. N/A Intron Variant
GAB3 transcript variant X1 XM_011531103.1:c. N/A Intron Variant
GAB3 transcript variant X6 XM_011531105.1:c. N/A Intron Variant
GAB3 transcript variant X7 XM_011531106.1:c. N/A Intron Variant
GAB3 transcript variant X3 XM_017029276.1:c. N/A Intron Variant
GAB3 transcript variant X8 XR_001755655.1:n. N/A Intron Variant
GAB3 transcript variant X2 XR_938505.1:n. 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

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 125568 G=0.37381 A=0.62619
gnomAD - Genomes Global Study-wide 21315 G=0.3617 A=0.6383
gnomAD - Genomes European Sub 13144 G=0.3214 A=0.6786
gnomAD - Genomes African Sub 5643 G=0.479 A=0.521
gnomAD - Genomes East Asian Sub 947 G=0.19 A=0.81
gnomAD - Genomes Other Sub 789 G=0.32 A=0.68
gnomAD - Genomes American Sub 615 G=0.45 A=0.55
gnomAD - Genomes Ashkenazi Jewish Sub 177 G=0.39 A=0.61
1000Genomes Global Study-wide 3775 G=0.353 A=0.647
1000Genomes African Sub 1003 G=0.484 A=0.516
1000Genomes Europe Sub 766 G=0.26 A=0.74
1000Genomes East Asian Sub 764 G=0.22 A=0.78
1000Genomes South Asian Sub 718 G=0.40 A=0.60
1000Genomes American Sub 524 G=0.36 A=0.64
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.329 A=0.671
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 G=0.333 A=0.667
A Vietnamese Genetic Variation Database Global Study-wide 48 G=0.1 A=0.9
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 Note
GRCh38.p12 chr X NC_000023.11:g.154717327= NC_000023.11:g.15471732...

NC_000023.11:g.154717327G>A

GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.2151306= NW_003871103.3:g.215130...

NW_003871103.3:g.2151306G>A

GAB3 RefSeqGene NG_012834.2:g.38747= NG_012834.2:g.38747C>T
GRCh37.p13 chr X NC_000023.10:g.153945602= NC_000023.10:g.15394560...

NC_000023.10:g.153945602G>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#.

96 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3758091 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss10563912 Jul 11, 2003 (116)
3 SSAHASNP ss21041808 Apr 05, 2004 (121)
4 ABI ss43609885 Mar 14, 2006 (126)
5 ILLUMINA ss66711878 Dec 02, 2006 (127)
6 ILLUMINA ss67266314 Dec 02, 2006 (127)
7 ILLUMINA ss67666280 Dec 02, 2006 (127)
8 ILLUMINA ss70744723 May 23, 2008 (130)
9 ILLUMINA ss71316250 May 18, 2007 (127)
10 ILLUMINA ss75622664 Dec 07, 2007 (129)
11 ILLUMINA ss79142607 Dec 14, 2007 (130)
12 HGSV ss83403173 Dec 14, 2007 (130)
13 KRIBB_YJKIM ss84066191 Dec 14, 2007 (130)
14 HGSV ss85256482 Dec 14, 2007 (130)
15 BCMHGSC_JDW ss94440138 Mar 25, 2008 (129)
16 BGI ss105777160 Feb 04, 2009 (130)
17 1000GENOMES ss113058145 Jan 25, 2009 (130)
18 1000GENOMES ss115338428 Jan 25, 2009 (130)
19 ILLUMINA ss122079780 Dec 01, 2009 (131)
20 ENSEMBL ss133697649 Dec 01, 2009 (131)
21 ENSEMBL ss144889517 Dec 01, 2009 (131)
22 ILLUMINA ss154226585 Dec 01, 2009 (131)
23 GMI ss157805439 Dec 01, 2009 (131)
24 ILLUMINA ss159403093 Dec 01, 2009 (131)
25 COMPLETE_GENOMICS ss163351995 Jul 04, 2010 (132)
26 COMPLETE_GENOMICS ss165817723 Jul 04, 2010 (132)
27 ILLUMINA ss171335114 Jul 04, 2010 (132)
28 ILLUMINA ss173422765 Jul 04, 2010 (132)
29 BUSHMAN ss204404364 Jul 04, 2010 (132)
30 BCM-HGSC-SUB ss208872141 Jul 04, 2010 (132)
31 ILLUMINA ss244291433 Jul 04, 2010 (132)
32 GMI ss283908974 May 04, 2012 (137)
33 GMI ss287660019 Apr 25, 2013 (138)
34 PJP ss294528440 May 09, 2011 (134)
35 1000GENOMES ss341909611 May 09, 2011 (134)
36 ILLUMINA ss410924892 Sep 17, 2011 (135)
37 EXOME_CHIP ss491580951 May 04, 2012 (137)
38 ILLUMINA ss537113879 Sep 11, 2015 (146)
39 TISHKOFF ss567108218 Apr 25, 2013 (138)
40 SSMP ss663088632 Apr 25, 2013 (138)
41 ILLUMINA ss780683761 Sep 11, 2015 (146)
42 ILLUMINA ss783357176 Sep 11, 2015 (146)
43 ILLUMINA ss825473125 Apr 01, 2015 (144)
44 ILLUMINA ss832914800 Jul 14, 2019 (153)
45 JMKIDD_LAB ss1083209465 Apr 09, 2015 (144)
46 DDI ss1432148149 Apr 09, 2015 (144)
47 1000GENOMES ss1556700715 Apr 09, 2015 (144)
48 EVA_GENOME_DK ss1583551895 Apr 09, 2015 (144)
49 EVA_UK10K_ALSPAC ss1641786279 Apr 09, 2015 (144)
50 EVA_UK10K_TWINSUK ss1684780312 Apr 09, 2015 (144)
51 ILLUMINA ss1752801608 Sep 11, 2015 (146)
52 ILLUMINA ss1917720720 Feb 17, 2016 (147)
53 WEILL_CORNELL_DGM ss1939852449 Feb 17, 2016 (147)
54 ILLUMINA ss1945981485 Feb 17, 2016 (147)
55 ILLUMINA ss1958229308 Feb 17, 2016 (147)
56 GENOMED ss1971457343 Sep 28, 2016 (149)
57 ILLUMINA ss2094837212 Oct 13, 2018 (152)
58 ILLUMINA ss2095002446 Dec 20, 2016 (150)
59 ILLUMINA ss2095228302 Oct 13, 2018 (152)
60 ILLUMINA ss2095228303 Oct 13, 2018 (152)
61 USC_VALOUEV ss2159307246 Oct 13, 2018 (152)
62 HUMAN_LONGEVITY ss2321329528 Dec 20, 2016 (150)
63 SYSTEMSBIOZJU ss2629800838 Oct 13, 2018 (152)
64 ILLUMINA ss2634991728 Oct 13, 2018 (152)
65 ILLUMINA ss2634991729 Oct 13, 2018 (152)
66 GRF ss2710419691 Oct 13, 2018 (152)
67 GNOMAD ss2984762969 Oct 13, 2018 (152)
68 AFFY ss2985493659 Oct 13, 2018 (152)
69 AFFY ss2986139345 Oct 13, 2018 (152)
70 SWEGEN ss3020826725 Oct 13, 2018 (152)
71 ILLUMINA ss3023047942 Oct 13, 2018 (152)
72 ILLUMINA ss3023047943 Oct 13, 2018 (152)
73 BIOINF_KMB_FNS_UNIBA ss3029146634 Nov 08, 2017 (151)
74 TOPMED ss3625308542 Nov 08, 2017 (151)
75 ILLUMINA ss3630501899 Oct 13, 2018 (152)
76 ILLUMINA ss3635263314 Oct 13, 2018 (152)
77 ILLUMINA ss3638884638 Oct 13, 2018 (152)
78 ILLUMINA ss3639440577 Oct 13, 2018 (152)
79 ILLUMINA ss3639756805 Oct 13, 2018 (152)
80 ILLUMINA ss3640970785 Oct 13, 2018 (152)
81 ILLUMINA ss3643808041 Oct 13, 2018 (152)
82 ILLUMINA ss3645020396 Oct 13, 2018 (152)
83 URBANLAB ss3651355017 Oct 13, 2018 (152)
84 ILLUMINA ss3653606249 Oct 13, 2018 (152)
85 ILLUMINA ss3653606250 Oct 13, 2018 (152)
86 ILLUMINA ss3653606251 Oct 13, 2018 (152)
87 ILLUMINA ss3654261410 Oct 13, 2018 (152)
88 ILLUMINA ss3726710925 Jul 14, 2019 (153)
89 ILLUMINA ss3744602569 Jul 14, 2019 (153)
90 ILLUMINA ss3745563817 Jul 14, 2019 (153)
91 EVA ss3770770784 Jul 14, 2019 (153)
92 ILLUMINA ss3773055423 Jul 14, 2019 (153)
93 PACBIO ss3788972373 Jul 14, 2019 (153)
94 PACBIO ss3793841524 Jul 14, 2019 (153)
95 PACBIO ss3798726489 Jul 14, 2019 (153)
96 KHV_HUMAN_GENOMES ss3823525798 Jul 14, 2019 (153)
97 1000Genomes NC_000023.10 - 153945602 Oct 13, 2018 (152)
98 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 153945602 Oct 13, 2018 (152)
99 gnomAD - Genomes NC_000023.10 - 153945602 Jul 14, 2019 (153)
100 TopMed NC_000023.11 - 154717327 Oct 13, 2018 (152)
101 UK 10K study - Twins NC_000023.10 - 153945602 Oct 13, 2018 (152)
102 A Vietnamese Genetic Variation Database NC_000023.10 - 153945602 Jul 14, 2019 (153)
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)
rs57416102 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83403173, ss85256482, ss3639440577, ss3639756805 NC_000023.8:153509305:G:A NC_000023.11:154717326:G:A (self)
ss94440138, ss113058145, ss115338428, ss163351995, ss165817723, ss204404364, ss208872141, ss283908974, ss287660019, ss294528440, ss825473125, ss2095002446, ss3643808041 NC_000023.9:153598795:G:A NC_000023.11:154717326:G:A (self)
84653916, 46613374, 229919103, 46613374, 10240176, ss341909611, ss491580951, ss537113879, ss567108218, ss663088632, ss780683761, ss783357176, ss832914800, ss1083209465, ss1432148149, ss1556700715, ss1583551895, ss1641786279, ss1684780312, ss1752801608, ss1917720720, ss1939852449, ss1945981485, ss1958229308, ss1971457343, ss2094837212, ss2095228302, ss2095228303, ss2159307246, ss2629800838, ss2634991728, ss2634991729, ss2710419691, ss2984762969, ss2985493659, ss2986139345, ss3020826725, ss3023047942, ss3023047943, ss3630501899, ss3635263314, ss3638884638, ss3640970785, ss3645020396, ss3653606249, ss3653606250, ss3653606251, ss3654261410, ss3744602569, ss3745563817, ss3770770784, ss3773055423, ss3788972373, ss3793841524, ss3798726489 NC_000023.10:153945601:G:A NC_000023.11:154717326:G:A (self)
439929105, ss2321329528, ss3029146634, ss3625308542, ss3651355017, ss3726710925, ss3823525798 NC_000023.11:154717326:G:A NC_000023.11:154717326:G:A (self)
ss10563912 NT_025965.11:1284527:G:A NC_000023.11:154717326:G:A (self)
ss21041808 NT_025965.12:1297223:G:A NC_000023.11:154717326:G:A (self)
ss3758091, ss43609885, ss66711878, ss67266314, ss67666280, ss70744723, ss71316250, ss75622664, ss79142607, ss84066191, ss105777160, ss122079780, ss133697649, ss144889517, ss154226585, ss157805439, ss159403093, ss171335114, ss173422765, ss244291433, ss410924892 NT_167198.1:4863539:G:A NC_000023.11:154717326: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.

7 citations for rs2664170
PMID Title Author Year Journal
19430480 Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Barrett JC et al. 2009 Nature genetics
20587799 Genetics of type 1 diabetes: what's next? Pociot F et al. 2010 Diabetes
20805105 Synthetic associations in the context of genome-wide association scan signals. Orozco G et al. 2010 Human molecular genetics
20885991 Advances and challenges in biomarker development for type 1 diabetes prediction and prevention using omic technologies. Carey C et al. 2010 Expert opinion on medical diagnostics
22278338 Confirmation of novel type 1 diabetes risk loci in families. Cooper JD et al. 2012 Diabetologia
22315323 Effects of non-HLA gene polymorphisms on development of islet autoimmunity and type 1 diabetes in a population with high-risk HLA-DR,DQ genotypes. Steck AK et al. 2012 Diabetes
26904692 Genetic Risk Score Modelling for Disease Progression in New-Onset Type 1 Diabetes Patients: Increased Genetic Load of Islet-Expressed and Cytokine-Regulated Candidate Genes Predicts Poorer Glycemic Control. Brorsson CA et al. 2016 Journal of diabetes research

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.post308+0fe9b3b