Name: rs11102637
Published: September 21, 2022
License: Open Access

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.

rs11102637

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113449170 (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=0.185024 (48974/264690, TOPMED)
A=0.173088 (24187/139738, GnomAD)
G=0.45865 (12957/28250, 14KJPN) (+ 19 more)
A=0.19626 (5376/27392, ALFA)
G=0.46080 (7723/16760, 8.3KJPN)
A=0.2402 (1538/6404, 1000G_30x)
A=0.2488 (1246/5008, 1000G)
A=0.1786 (800/4480, Estonian)
A=0.1554 (599/3854, ALSPAC)
A=0.1653 (613/3708, TWINSUK)
G=0.3570 (1046/2930, KOREAN)
G=0.3466 (635/1832, Korea1K)
A=0.1989 (226/1136, Daghestan)
A=0.144 (144/998, GoNL)
G=0.305 (236/774, PRJEB37584)
A=0.182 (109/600, NorthernSweden)
A=0.233 (76/326, HapMap)
G=0.381 (90/236, SGDP_PRJ)
A=0.181 (39/216, Qatari)
G=0.444 (96/216, Vietnamese)
A=0.12 (5/40, GENOME_DK)
G=0.33 (6/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MAGI3 : Intron Variant
Publications: 1 citation
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	27392	G=0.80374	A=0.19626
European	Sub	15888	G=0.83321	A=0.16679
African	Sub	3252	G=0.8675	A=0.1325
African Others	Sub	114	G=0.895	A=0.105
African American	Sub	3138	G=0.8665	A=0.1335
Asian	Sub	136	G=0.390	A=0.610
East Asian	Sub	106	G=0.311	A=0.689
Other Asian	Sub	30	G=0.67	A=0.33
Latin American 1	Sub	222	G=0.770	A=0.230
Latin American 2	Sub	4706	G=0.6496	A=0.3504
South Asian	Sub	116	G=0.905	A=0.095
Other	Sub	3072	G=0.8369	A=0.1631

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.814976	A=0.185024
gnomAD - Genomes	Global	Study-wide	139738	G=0.826912	A=0.173088
gnomAD - Genomes	European	Sub	75732	G=0.83047	A=0.16953
gnomAD - Genomes	African	Sub	41834	G=0.87644	A=0.12356
gnomAD - Genomes	American	Sub	13594	G=0.76674	A=0.23326
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.8222	A=0.1778
gnomAD - Genomes	East Asian	Sub	3116	G=0.3533	A=0.6467
gnomAD - Genomes	Other	Sub	2144	G=0.8120	A=0.1880
14KJPN	JAPANESE	Study-wide	28250	G=0.45865	A=0.54135
Allele Frequency Aggregator	Total	Global	27392	G=0.80374	A=0.19626
Allele Frequency Aggregator	European	Sub	15888	G=0.83321	A=0.16679
Allele Frequency Aggregator	Latin American 2	Sub	4706	G=0.6496	A=0.3504
Allele Frequency Aggregator	African	Sub	3252	G=0.8675	A=0.1325
Allele Frequency Aggregator	Other	Sub	3072	G=0.8369	A=0.1631
Allele Frequency Aggregator	Latin American 1	Sub	222	G=0.770	A=0.230
Allele Frequency Aggregator	Asian	Sub	136	G=0.390	A=0.610
Allele Frequency Aggregator	South Asian	Sub	116	G=0.905	A=0.095
8.3KJPN	JAPANESE	Study-wide	16760	G=0.46080	A=0.53920
1000Genomes_30x	Global	Study-wide	6404	G=0.7598	A=0.2402
1000Genomes_30x	African	Sub	1786	G=0.9087	A=0.0913
1000Genomes_30x	Europe	Sub	1266	G=0.8302	A=0.1698
1000Genomes_30x	South Asian	Sub	1202	G=0.8677	A=0.1323
1000Genomes_30x	East Asian	Sub	1170	G=0.3932	A=0.6068
1000Genomes_30x	American	Sub	980	G=0.703	A=0.297
1000Genomes	Global	Study-wide	5008	G=0.7512	A=0.2488
1000Genomes	African	Sub	1322	G=0.9070	A=0.0930
1000Genomes	East Asian	Sub	1008	G=0.3978	A=0.6022
1000Genomes	Europe	Sub	1006	G=0.8250	A=0.1750
1000Genomes	South Asian	Sub	978	G=0.869	A=0.131
1000Genomes	American	Sub	694	G=0.695	A=0.305
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8214	A=0.1786
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8446	A=0.1554
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8347	A=0.1653
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.3570	A=0.6430
Korean Genome Project	KOREAN	Study-wide	1832	G=0.3466	A=0.6534
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	G=0.8011	A=0.1989
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	G=0.820	A=0.180
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	G=0.854	A=0.146
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	G=0.598	A=0.402
Genome-wide autozygosity in Daghestan	Europe	Sub	108	G=0.759	A=0.241
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	G=0.89	A=0.11
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	G=0.83	A=0.17
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.856	A=0.144
CNV burdens in cranial meningiomas	Global	Study-wide	774	G=0.305	A=0.695
CNV burdens in cranial meningiomas	CRM	Sub	774	G=0.305	A=0.695
Northern Sweden	ACPOP	Study-wide	600	G=0.818	A=0.182
HapMap	Global	Study-wide	326	G=0.767	A=0.233
HapMap	American	Sub	120	G=0.833	A=0.167
HapMap	African	Sub	118	G=0.898	A=0.102
HapMap	Asian	Sub	88	G=0.50	A=0.50
SGDP_PRJ	Global	Study-wide	236	G=0.381	A=0.619
Qatari	Global	Study-wide	216	G=0.819	A=0.181
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.444	A=0.556
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	A=0.12
Siberian	Global	Study-wide	18	G=0.33	A=0.67

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 1	NC_000001.11:g.113449170G>A
GRCh37.p13 chr 1	NC_000001.10:g.113991792G>A

Gene: MAGI3, membrane associated guanylate kinase, WW and PDZ domain containing 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAGI3 transcript variant 1	NM_001142782.2:c.316+5782… NM_001142782.2:c.316+57821G>A	N/A	Intron Variant
MAGI3 transcript variant 2	NM_152900.3:c.316+57821G>A	N/A	Intron Variant
MAGI3 transcript variant X2	XM_005270737.4:c.316+5782… XM_005270737.4:c.316+57821G>A	N/A	Intron Variant
MAGI3 transcript variant X1	XM_017000974.2:c.316+5782… XM_017000974.2:c.316+57821G>A	N/A	Intron Variant
MAGI3 transcript variant X3	XM_047417371.1:c.316+5782… XM_047417371.1:c.316+57821G>A	N/A	Intron Variant

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

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 1	NC_000001.11:g.113449170=	NC_000001.11:g.113449170G>A
GRCh37.p13 chr 1	NC_000001.10:g.113991792=	NC_000001.10:g.113991792G>A
MAGI3 transcript variant 1	NM_001142782.1:c.316+57821=	NM_001142782.1:c.316+57821G>A
MAGI3 transcript variant 1	NM_001142782.2:c.316+57821=	NM_001142782.2:c.316+57821G>A
MAGI3 transcript variant 2	NM_152900.2:c.316+57821=	NM_152900.2:c.316+57821G>A
MAGI3 transcript variant 2	NM_152900.3:c.316+57821=	NM_152900.3:c.316+57821G>A
MAGI3 transcript variant X1	XM_005270736.1:c.316+57821=	XM_005270736.1:c.316+57821G>A
MAGI3 transcript variant X2	XM_005270737.1:c.316+57821=	XM_005270737.1:c.316+57821G>A
MAGI3 transcript variant X2	XM_005270737.4:c.316+57821=	XM_005270737.4:c.316+57821G>A
MAGI3 transcript variant X1	XM_017000974.2:c.316+57821=	XM_017000974.2:c.316+57821G>A
MAGI3 transcript variant X3	XM_047417371.1:c.316+57821=	XM_047417371.1:c.316+57821G>A

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#.

71 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18116294	Feb 27, 2004 (120)
2	CSHL-HAPMAP	ss19867747	Feb 27, 2004 (120)
3	SSAHASNP	ss20513295	Apr 05, 2004 (121)
4	ABI	ss41181678	Mar 15, 2006 (126)
5	HGSV	ss78461430	Dec 07, 2007 (129)
6	1000GENOMES	ss108536416	Jan 23, 2009 (130)
7	GMI	ss155550512	Dec 01, 2009 (131)
8	ILLUMINA	ss161038169	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss165056194	Jul 04, 2010 (132)
10	1000GENOMES	ss218605678	Jul 14, 2010 (132)
11	1000GENOMES	ss230698080	Jul 14, 2010 (132)
12	1000GENOMES	ss238354536	Jul 15, 2010 (132)
13	BL	ss253395960	May 09, 2011 (134)
14	GMI	ss275984099	May 04, 2012 (137)
15	GMI	ss284124018	Apr 25, 2013 (138)
16	ILLUMINA	ss479386970	Sep 08, 2015 (146)
17	TISHKOFF	ss554593617	Apr 25, 2013 (138)
18	SSMP	ss648322942	Apr 25, 2013 (138)
19	EVA-GONL	ss975586358	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1068204834	Aug 21, 2014 (142)
21	1000GENOMES	ss1292493527	Aug 21, 2014 (142)
22	HAMMER_LAB	ss1397257889	Sep 08, 2015 (146)
23	DDI	ss1425942002	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1574333318	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1601022979	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1644017012	Apr 01, 2015 (144)
27	WEILL_CORNELL_DGM	ss1918786691	Feb 12, 2016 (147)
28	GENOMED	ss1966845146	Jul 19, 2016 (147)
29	JJLAB	ss2019917803	Sep 14, 2016 (149)
30	ILLUMINA	ss2094846805	Dec 20, 2016 (150)
31	ILLUMINA	ss2094971891	Dec 20, 2016 (150)
32	USC_VALOUEV	ss2147936492	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2165839020	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2624468533	Nov 08, 2017 (151)
35	GRF	ss2697866787	Nov 08, 2017 (151)
36	GNOMAD	ss2759733444	Nov 08, 2017 (151)
37	SWEGEN	ss2987463675	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3023723407	Nov 08, 2017 (151)
39	CSHL	ss3343642310	Nov 08, 2017 (151)
40	ILLUMINA	ss3636021886	Oct 11, 2018 (152)
41	ILLUMINA	ss3651454848	Oct 11, 2018 (152)
42	EGCUT_WGS	ss3655552616	Jul 12, 2019 (153)
43	EVA_DECODE	ss3687561312	Jul 12, 2019 (153)
44	ACPOP	ss3727401994	Jul 12, 2019 (153)
45	EVA	ss3746691092	Jul 12, 2019 (153)
46	PACBIO	ss3783524146	Jul 12, 2019 (153)
47	PACBIO	ss3789165308	Jul 12, 2019 (153)
48	PACBIO	ss3794038244	Jul 12, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3799693964	Jul 12, 2019 (153)
50	EVA	ss3826378064	Apr 25, 2020 (154)
51	EVA	ss3836580721	Apr 25, 2020 (154)
52	EVA	ss3841989157	Apr 25, 2020 (154)
53	SGDP_PRJ	ss3849681758	Apr 25, 2020 (154)
54	KRGDB	ss3894779448	Apr 25, 2020 (154)
55	KOGIC	ss3945278724	Apr 25, 2020 (154)
56	EVA	ss3984463224	Apr 25, 2021 (155)
57	TOPMED	ss4464138663	Apr 25, 2021 (155)
58	TOMMO_GENOMICS	ss5145750231	Apr 25, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5243662603	Oct 12, 2022 (156)
60	EVA	ss5321281173	Oct 12, 2022 (156)
61	HUGCELL_USP	ss5444580739	Oct 12, 2022 (156)
62	EVA	ss5506002149	Oct 12, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5516682775	Oct 12, 2022 (156)
64	SANFORD_IMAGENETICS	ss5626328877	Oct 12, 2022 (156)
65	TOMMO_GENOMICS	ss5671039395	Oct 12, 2022 (156)
66	YY_MCH	ss5800945000	Oct 12, 2022 (156)
67	EVA	ss5832504722	Oct 12, 2022 (156)
68	EVA	ss5849074125	Oct 12, 2022 (156)
69	EVA	ss5909862099	Oct 12, 2022 (156)
70	EVA	ss5938196362	Oct 12, 2022 (156)
71	EVA	ss5979979365	Oct 12, 2022 (156)
72	1000Genomes	NC_000001.10 - 113991792	Oct 11, 2018 (152)
73	1000Genomes_30x	NC_000001.11 - 113449170	Oct 12, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 113991792	Oct 11, 2018 (152)
75	Genome-wide autozygosity in Daghestan	NC_000001.9 - 113793315	Apr 25, 2020 (154)
76	Genetic variation in the Estonian population	NC_000001.10 - 113991792	Oct 11, 2018 (152)
77	The Danish reference pan genome	NC_000001.10 - 113991792	Apr 25, 2020 (154)
78	gnomAD - Genomes	NC_000001.11 - 113449170	Apr 25, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000001.10 - 113991792	Apr 25, 2020 (154)
80	HapMap	NC_000001.11 - 113449170	Apr 25, 2020 (154)
81	KOREAN population from KRGDB	NC_000001.10 - 113991792	Apr 25, 2020 (154)
82	Korean Genome Project	NC_000001.11 - 113449170	Apr 25, 2020 (154)
83	Northern Sweden	NC_000001.10 - 113991792	Jul 12, 2019 (153)
84	CNV burdens in cranial meningiomas	NC_000001.10 - 113991792	Apr 25, 2021 (155)
85	Qatari	NC_000001.10 - 113991792	Apr 25, 2020 (154)
86	SGDP_PRJ	NC_000001.10 - 113991792	Apr 25, 2020 (154)
87	Siberian	NC_000001.10 - 113991792	Apr 25, 2020 (154)
88	8.3KJPN	NC_000001.10 - 113991792	Apr 25, 2021 (155)
89	14KJPN	NC_000001.11 - 113449170	Oct 12, 2022 (156)
90	TopMed	NC_000001.11 - 113449170	Apr 25, 2021 (155)
91	UK 10K study - Twins	NC_000001.10 - 113991792	Oct 11, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000001.10 - 113991792	Jul 12, 2019 (153)
93	ALFA	NC_000001.11 - 113449170	Apr 25, 2021 (155)

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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78461430	NC_000001.8:113703833:G:A	NC_000001.11:113449169:G:A	(self)
19165, ss108536416, ss165056194, ss253395960, ss275984099, ss284124018, ss1397257889, ss2094846805	NC_000001.9:113793314:G:A	NC_000001.11:113449169:G:A	(self)
3271575, 1810126, 1290864, 1671175, 787238, 1956842, 686859, 12536, 828621, 1698738, 452846, 3719538, 1810126, 391953, ss218605678, ss230698080, ss238354536, ss479386970, ss554593617, ss648322942, ss975586358, ss1068204834, ss1292493527, ss1425942002, ss1574333318, ss1601022979, ss1644017012, ss1918786691, ss1966845146, ss2019917803, ss2094971891, ss2147936492, ss2624468533, ss2697866787, ss2759733444, ss2987463675, ss3343642310, ss3636021886, ss3651454848, ss3655552616, ss3727401994, ss3746691092, ss3783524146, ss3789165308, ss3794038244, ss3826378064, ss3836580721, ss3849681758, ss3894779448, ss3984463224, ss5145750231, ss5321281173, ss5506002149, ss5626328877, ss5832504722, ss5938196362, ss5979979365	NC_000001.10:113991791:G:A	NC_000001.11:113449169:G:A	(self)
4208710, 23136239, 158167, 1656725, 4876499, 27744998, 2090288302, ss2165839020, ss3023723407, ss3687561312, ss3799693964, ss3841989157, ss3945278724, ss4464138663, ss5243662603, ss5444580739, ss5516682775, ss5671039395, ss5800945000, ss5849074125, ss5909862099	NC_000001.11:113449169:G:A	NC_000001.11:113449169:G:A	(self)
ss18116294, ss19867747, ss20513295	NT_019273.16:4987739:G:A	NC_000001.11:113449169:G:A	(self)
ss41181678, ss155550512, ss161038169	NT_032977.9:83963709:G:A	NC_000001.11:113449169:G:A	(self)

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

1 citation for rs11102637

PMID	Title	Author	Year	Journal
24918582	Dense genotyping of immune-related loci identifies variants associated with clearance of HPV among HIV-positive women in the HIV epidemiology research study (HERS).	Sudenga SL et al.	2014	PloS one

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs11102637