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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.

rs357116

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:13280352 (GRCh38.p13) 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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.495157 (131063/264690, TOPMED)
A=0.464399 (70702/152244, ALFA)
A=0.489819 (68604/140060, GnomAD) (+ 16 more)
A=0.37894 (6351/16760, 8.3KJPN)
A=0.4946 (2477/5008, 1000G)
A=0.4094 (1834/4480, Estonian)
A=0.4344 (1674/3854, ALSPAC)
A=0.4512 (1673/3708, TWINSUK)
A=0.3771 (1105/2930, KOREAN)
G=0.4582 (867/1892, HapMap)
A=0.3826 (701/1832, Korea1K)
A=0.444 (443/998, GoNL)
A=0.430 (258/600, NorthernSweden)
A=0.294 (127/432, SGDP_PRJ)
G=0.477 (103/216, Qatari)
G=0.495 (105/212, Vietnamese)
A=0.39 (22/56, Ancient Sardinia)
A=0.39 (17/44, Siberian)
A=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IQSEC1 : Intron Variant
Publications
0 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.p13 chr 3 NC_000003.12:g.13280352A>G
GRCh38.p13 chr 3 NC_000003.12:g.13280352A>T
GRCh37.p13 chr 3 NC_000003.11:g.13321852A>G
GRCh37.p13 chr 3 NC_000003.11:g.13321852A>T
Gene: IQSEC1, IQ motif and Sec7 domain ArfGEF 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IQSEC1 transcript variant 4 NM_001376938.2:c.272+2359…

NM_001376938.2:c.272+2359T>C

N/A Intron Variant
IQSEC1 transcript variant 1 NM_001134382.3:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant 3 NM_001330619.3:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant 2 NM_014869.8:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X2 XM_011534305.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X3 XM_011534306.3:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X4 XM_011534307.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X5 XM_011534308.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X7 XM_011534311.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X8 XM_011534312.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X10 XM_011534313.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X9 XM_011534314.2:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X1 XM_024453845.1:c. N/A Genic Upstream Transcript Variant
IQSEC1 transcript variant X6 XM_024453846.1:c. N/A Genic Upstream Transcript 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 152244 A=0.464399 G=0.535601
European Sub 127966 A=0.460661 G=0.539339
African Sub 7324 A=0.5881 G=0.4119
African Others Sub 250 A=0.668 G=0.332
African American Sub 7074 A=0.5852 G=0.4148
Asian Sub 670 A=0.449 G=0.551
East Asian Sub 506 A=0.451 G=0.549
Other Asian Sub 164 A=0.445 G=0.555
Latin American 1 Sub 884 A=0.483 G=0.517
Latin American 2 Sub 8430 A=0.4204 G=0.5796
South Asian Sub 196 A=0.510 G=0.490
Other Sub 6774 A=0.4538 G=0.5462


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=0.495157 G=0.504843
gnomAD - Genomes Global Study-wide 140060 A=0.489819 G=0.510181
gnomAD - Genomes European Sub 75858 A=0.44304 G=0.55696
gnomAD - Genomes African Sub 41948 A=0.58866 G=0.41134
gnomAD - Genomes American Sub 13660 A=0.46611 G=0.53389
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.4443 G=0.5557
gnomAD - Genomes East Asian Sub 3124 A=0.4405 G=0.5595
gnomAD - Genomes Other Sub 2150 A=0.5047 G=0.4953
8.3KJPN JAPANESE Study-wide 16760 A=0.37894 G=0.62106
1000Genomes Global Study-wide 5008 A=0.4946 G=0.5054
1000Genomes African Sub 1322 A=0.6490 G=0.3510
1000Genomes East Asian Sub 1008 A=0.4464 G=0.5536
1000Genomes Europe Sub 1006 A=0.4304 G=0.5696
1000Genomes South Asian Sub 978 A=0.462 G=0.538
1000Genomes American Sub 694 A=0.409 G=0.591
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4094 G=0.5906
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4344 G=0.5656
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4512 G=0.5488
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.3771 G=0.6229, T=0.0000
HapMap Global Study-wide 1892 A=0.5418 G=0.4582
HapMap American Sub 770 A=0.491 G=0.509
HapMap African Sub 692 A=0.656 G=0.344
HapMap Asian Sub 254 A=0.441 G=0.559
HapMap Europe Sub 176 A=0.460 G=0.540
Korean Genome Project KOREAN Study-wide 1832 A=0.3826 G=0.6174
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.444 G=0.556
Northern Sweden ACPOP Study-wide 600 A=0.430 G=0.570
SGDP_PRJ Global Study-wide 432 A=0.294 G=0.706
Qatari Global Study-wide 216 A=0.523 G=0.477
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.505 G=0.495
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 56 A=0.39 G=0.61
Siberian Global Study-wide 44 A=0.39 G=0.61
The Danish reference pan genome Danish Study-wide 40 A=0.35 G=0.65
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= G T
GRCh38.p13 chr 3 NC_000003.12:g.13280352= NC_000003.12:g.13280352A>G NC_000003.12:g.13280352A>T
GRCh37.p13 chr 3 NC_000003.11:g.13321852= NC_000003.11:g.13321852A>G NC_000003.11:g.13321852A>T
IQSEC1 transcript variant 4 NM_001376938.2:c.272+2359= NM_001376938.2:c.272+2359T>C NM_001376938.2:c.272+2359T>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#.

100 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss453353 Jul 12, 2000 (79)
2 SC_JCM ss850284 Aug 11, 2000 (85)
3 KWOK ss892303 Oct 04, 2000 (86)
4 KWOK ss898809 Oct 04, 2000 (86)
5 KWOK ss1001652 Oct 04, 2000 (86)
6 KWOK ss1003671 Oct 04, 2000 (86)
7 KWOK ss1623667 Oct 18, 2000 (87)
8 KWOK ss1649579 Oct 18, 2000 (87)
9 ILLUMINA ss65718552 Oct 16, 2006 (127)
10 AFFY ss66432859 Dec 01, 2006 (127)
11 PERLEGEN ss68853389 May 18, 2007 (127)
12 AFFY ss76207237 Dec 07, 2007 (129)
13 KRIBB_YJKIM ss81418664 Dec 15, 2007 (130)
14 HGSV ss83328128 Dec 15, 2007 (130)
15 BCMHGSC_JDW ss92002732 Mar 24, 2008 (129)
16 BGI ss103903225 Dec 01, 2009 (131)
17 1000GENOMES ss111279209 Jan 25, 2009 (130)
18 ILLUMINA ss120244559 Dec 01, 2009 (131)
19 ENSEMBL ss138730532 Dec 01, 2009 (131)
20 ILLUMINA ss160628491 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss161926885 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss166185206 Jul 04, 2010 (132)
23 AFFY ss172813492 Jul 04, 2010 (132)
24 ILLUMINA ss173604041 Jul 04, 2010 (132)
25 BUSHMAN ss202156735 Jul 04, 2010 (132)
26 BCM-HGSC-SUB ss206146624 Jul 04, 2010 (132)
27 1000GENOMES ss219988513 Jul 14, 2010 (132)
28 1000GENOMES ss231713774 Jul 14, 2010 (132)
29 1000GENOMES ss239146763 Jul 15, 2010 (132)
30 ILLUMINA ss244256166 Jul 04, 2010 (132)
31 GMI ss277019368 May 04, 2012 (137)
32 GMI ss284597890 Apr 25, 2013 (138)
33 PJP ss292935341 May 09, 2011 (134)
34 ILLUMINA ss480793660 May 04, 2012 (137)
35 ILLUMINA ss480809376 May 04, 2012 (137)
36 ILLUMINA ss481728697 Sep 08, 2015 (146)
37 ILLUMINA ss485191610 May 04, 2012 (137)
38 ILLUMINA ss537180619 Sep 08, 2015 (146)
39 TISHKOFF ss556435642 Apr 25, 2013 (138)
40 SSMP ss650102681 Apr 25, 2013 (138)
41 ILLUMINA ss778520058 Aug 21, 2014 (142)
42 ILLUMINA ss783041854 Aug 21, 2014 (142)
43 ILLUMINA ss784001064 Aug 21, 2014 (142)
44 ILLUMINA ss832299611 Apr 01, 2015 (144)
45 ILLUMINA ss833976449 Aug 21, 2014 (142)
46 EVA-GONL ss978287498 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1070186103 Aug 21, 2014 (142)
48 1000GENOMES ss1302862051 Aug 21, 2014 (142)
49 DDI ss1429335204 Apr 01, 2015 (144)
50 EVA_GENOME_DK ss1579851166 Apr 01, 2015 (144)
51 EVA_DECODE ss1587749101 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1606446361 Apr 01, 2015 (144)
53 EVA_UK10K_TWINSUK ss1649440394 Apr 01, 2015 (144)
54 EVA_SVP ss1712555031 Apr 01, 2015 (144)
55 ILLUMINA ss1752440556 Sep 08, 2015 (146)
56 HAMMER_LAB ss1798882839 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1921540195 Feb 12, 2016 (147)
58 GENOMED ss1969326927 Jul 19, 2016 (147)
59 JJLAB ss2021323582 Sep 14, 2016 (149)
60 USC_VALOUEV ss2149391250 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2249195662 Dec 20, 2016 (150)
62 TOPMED ss2416239480 Dec 20, 2016 (150)
63 SYSTEMSBIOZJU ss2625161695 Nov 08, 2017 (151)
64 ILLUMINA ss2633913793 Nov 08, 2017 (151)
65 GRF ss2704752151 Nov 08, 2017 (151)
66 GNOMAD ss2789698909 Nov 08, 2017 (151)
67 SWEGEN ss2991853376 Nov 08, 2017 (151)
68 BIOINF_KMB_FNS_UNIBA ss3024424646 Nov 08, 2017 (151)
69 CSHL ss3344892470 Nov 08, 2017 (151)
70 TOPMED ss3383047469 Nov 08, 2017 (151)
71 ILLUMINA ss3628593988 Oct 11, 2018 (152)
72 ILLUMINA ss3631862191 Oct 11, 2018 (152)
73 ILLUMINA ss3633282752 Oct 11, 2018 (152)
74 ILLUMINA ss3633999263 Oct 11, 2018 (152)
75 ILLUMINA ss3634881251 Oct 11, 2018 (152)
76 ILLUMINA ss3635683438 Oct 11, 2018 (152)
77 ILLUMINA ss3636577432 Oct 11, 2018 (152)
78 ILLUMINA ss3637435742 Oct 11, 2018 (152)
79 ILLUMINA ss3638398195 Oct 11, 2018 (152)
80 ILLUMINA ss3640588554 Oct 11, 2018 (152)
81 EGCUT_WGS ss3659753938 Jul 13, 2019 (153)
82 EVA_DECODE ss3708666288 Jul 13, 2019 (153)
83 ACPOP ss3729644651 Jul 13, 2019 (153)
84 ILLUMINA ss3745181048 Jul 13, 2019 (153)
85 EVA ss3759680178 Jul 13, 2019 (153)
86 ILLUMINA ss3772676835 Jul 13, 2019 (153)
87 PACBIO ss3784239389 Jul 13, 2019 (153)
88 PACBIO ss3789767476 Jul 13, 2019 (153)
89 PACBIO ss3794641238 Jul 13, 2019 (153)
90 KHV_HUMAN_GENOMES ss3802828801 Jul 13, 2019 (153)
91 EVA ss3827669138 Apr 25, 2020 (154)
92 EVA ss3837256656 Apr 25, 2020 (154)
93 EVA ss3842680640 Apr 25, 2020 (154)
94 SGDP_PRJ ss3855258174 Apr 25, 2020 (154)
95 KRGDB ss3901033757 Apr 25, 2020 (154)
96 KOGIC ss3950693952 Apr 25, 2020 (154)
97 EVA ss3984974000 Apr 26, 2021 (155)
98 EVA ss4017065866 Apr 26, 2021 (155)
99 TOPMED ss4554703745 Apr 26, 2021 (155)
100 TOMMO_GENOMICS ss5157865826 Apr 26, 2021 (155)
101 1000Genomes NC_000003.11 - 13321852 Oct 11, 2018 (152)
102 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 13321852 Oct 11, 2018 (152)
103 Genetic variation in the Estonian population NC_000003.11 - 13321852 Oct 11, 2018 (152)
104 The Danish reference pan genome NC_000003.11 - 13321852 Apr 25, 2020 (154)
105 gnomAD - Genomes NC_000003.12 - 13280352 Apr 26, 2021 (155)
106 Genome of the Netherlands Release 5 NC_000003.11 - 13321852 Apr 25, 2020 (154)
107 HapMap NC_000003.12 - 13280352 Apr 25, 2020 (154)
108 KOREAN population from KRGDB NC_000003.11 - 13321852 Apr 25, 2020 (154)
109 Korean Genome Project NC_000003.12 - 13280352 Apr 25, 2020 (154)
110 Northern Sweden NC_000003.11 - 13321852 Jul 13, 2019 (153)
111 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000003.11 - 13321852 Apr 26, 2021 (155)
112 Qatari NC_000003.11 - 13321852 Apr 25, 2020 (154)
113 SGDP_PRJ NC_000003.11 - 13321852 Apr 25, 2020 (154)
114 Siberian NC_000003.11 - 13321852 Apr 25, 2020 (154)
115 8.3KJPN NC_000003.11 - 13321852 Apr 26, 2021 (155)
116 TopMed NC_000003.12 - 13280352 Apr 26, 2021 (155)
117 UK 10K study - Twins NC_000003.11 - 13321852 Oct 11, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000003.11 - 13321852 Jul 13, 2019 (153)
119 ALFA NC_000003.12 - 13280352 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)
rs676781 Sep 19, 2000 (85)
rs58568633 May 24, 2008 (130)
rs60647975 Feb 26, 2009 (130)
rs386583974 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83328128 NC_000003.9:13296851:A:G NC_000003.12:13280351:A:G (self)
ss92002732, ss111279209, ss160628491, ss161926885, ss166185206, ss202156735, ss206146624, ss244256166, ss277019368, ss284597890, ss292935341, ss480793660, ss1587749101, ss1712555031 NC_000003.10:13296851:A:G NC_000003.12:13280351:A:G (self)
14009054, 7766568, 5492186, 6016105, 3409745, 8211151, 2929516, 199927, 3582125, 7275154, 1907604, 15835133, 7766568, 1690801, ss219988513, ss231713774, ss239146763, ss480809376, ss481728697, ss485191610, ss537180619, ss556435642, ss650102681, ss778520058, ss783041854, ss784001064, ss832299611, ss833976449, ss978287498, ss1070186103, ss1302862051, ss1429335204, ss1579851166, ss1606446361, ss1649440394, ss1752440556, ss1798882839, ss1921540195, ss1969326927, ss2021323582, ss2149391250, ss2416239480, ss2625161695, ss2633913793, ss2704752151, ss2789698909, ss2991853376, ss3344892470, ss3628593988, ss3631862191, ss3633282752, ss3633999263, ss3634881251, ss3635683438, ss3636577432, ss3637435742, ss3638398195, ss3640588554, ss3659753938, ss3729644651, ss3745181048, ss3759680178, ss3772676835, ss3784239389, ss3789767476, ss3794641238, ss3827669138, ss3837256656, ss3855258174, ss3901033757, ss3984974000, ss4017065866, ss5157865826 NC_000003.11:13321851:A:G NC_000003.12:13280351:A:G (self)
99454668, 2305809, 7071953, 244971533, 392081300, 13609333790, ss2249195662, ss3024424646, ss3383047469, ss3708666288, ss3802828801, ss3842680640, ss3950693952, ss4554703745 NC_000003.12:13280351:A:G NC_000003.12:13280351:A:G (self)
ss453353, ss850284, ss892303, ss898809, ss1001652, ss1003671, ss1623667, ss1649579, ss65718552, ss66432859, ss68853389, ss76207237, ss81418664, ss103903225, ss120244559, ss138730532, ss172813492, ss173604041 NT_022517.18:13261851:A:G NC_000003.12:13280351:A:G (self)
8211151, ss3901033757 NC_000003.11:13321851:A:T NC_000003.12:13280351:A:T (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 rs357116

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.post596+ae089ad