Name: rs12753351
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.

rs12753351

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113639972 (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 / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.207896 (55028/264690, TOPMED)
A=0.07071 (1998/28256, 14KJPN)
A=0.07339 (1230/16760, 8.3KJPN) (+ 15 more)
A=0.12733 (1788/14042, ALFA)
A=0.1933 (1238/6404, 1000G_30x)
A=0.1959 (981/5008, 1000G)
A=0.2299 (1030/4480, Estonian)
A=0.2976 (1147/3854, ALSPAC)
A=0.2886 (1070/3708, TWINSUK)
A=0.0886 (259/2922, KOREAN)
A=0.0655 (120/1832, Korea1K)
A=0.279 (278/998, GoNL)
A=0.248 (149/600, NorthernSweden)
A=0.315 (68/216, Qatari)
A=0.187 (40/214, Vietnamese)
G=0.386 (78/202, SGDP_PRJ)
A=0.33 (13/40, GENOME_DK)
G=0.47 (14/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MAGI3 : Intron 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	14042	G=0.87267	A=0.12733, C=0.00000, T=0.00000
European	Sub	10362	G=0.83546	A=0.16454, C=0.00000, T=0.00000
African	Sub	2610	G=0.9954	A=0.0046, C=0.0000, T=0.0000
African Others	Sub	114	G=1.000	A=0.000, C=0.000, T=0.000
African American	Sub	2496	G=0.9952	A=0.0048, C=0.0000, T=0.0000
Asian	Sub	82	G=0.99	A=0.01, C=0.00, T=0.00
East Asian	Sub	66	G=1.00	A=0.00, C=0.00, T=0.00
Other Asian	Sub	16	G=0.94	A=0.06, C=0.00, T=0.00
Latin American 1	Sub	82	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 2	Sub	358	G=1.000	A=0.000, C=0.000, T=0.000
South Asian	Sub	34	G=0.91	A=0.09, C=0.00, T=0.00
Other	Sub	514	G=0.870	A=0.130, C=0.000, T=0.000

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=0.792104	A=0.207896
14KJPN	JAPANESE	Study-wide	28256	G=0.92929	A=0.07071
8.3KJPN	JAPANESE	Study-wide	16760	G=0.92661	A=0.07339
Allele Frequency Aggregator	Total	Global	14042	G=0.87267	A=0.12733, C=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	10362	G=0.83546	A=0.16454, C=0.00000, T=0.00000
Allele Frequency Aggregator	African	Sub	2610	G=0.9954	A=0.0046, C=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	514	G=0.870	A=0.130, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	358	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	82	G=1.00	A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	82	G=0.99	A=0.01, C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	34	G=0.91	A=0.09, C=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8067	A=0.1933
1000Genomes_30x	African	Sub	1786	G=0.9888	A=0.0112
1000Genomes_30x	Europe	Sub	1266	G=0.6746	A=0.3254
1000Genomes_30x	South Asian	Sub	1202	G=0.5948	A=0.4052
1000Genomes_30x	East Asian	Sub	1170	G=0.9043	A=0.0957
1000Genomes_30x	American	Sub	980	G=0.789	A=0.211
1000Genomes	Global	Study-wide	5008	G=0.8041	A=0.1959
1000Genomes	African	Sub	1322	G=0.9864	A=0.0136
1000Genomes	East Asian	Sub	1008	G=0.9067	A=0.0933
1000Genomes	Europe	Sub	1006	G=0.6730	A=0.3270
1000Genomes	South Asian	Sub	978	G=0.592	A=0.408
1000Genomes	American	Sub	694	G=0.797	A=0.203
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7701	A=0.2299
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7024	A=0.2976
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7114	A=0.2886
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9114	A=0.0886
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9345	A=0.0655
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.721	A=0.279
Northern Sweden	ACPOP	Study-wide	600	G=0.752	A=0.248
Qatari	Global	Study-wide	216	G=0.685	A=0.315
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.813	A=0.187
SGDP_PRJ	Global	Study-wide	202	G=0.386	A=0.614
The Danish reference pan genome	Danish	Study-wide	40	G=0.68	A=0.33
Siberian	Global	Study-wide	30	G=0.47	A=0.53

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.113639972G>A
GRCh38.p14 chr 1	NC_000001.11:g.113639972G>C
GRCh38.p14 chr 1	NC_000001.11:g.113639972G>T
GRCh37.p13 chr 1	NC_000001.10:g.114182594G>A
GRCh37.p13 chr 1	NC_000001.10:g.114182594G>C
GRCh37.p13 chr 1	NC_000001.10:g.114182594G>T

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.1361-193… NM_001142782.2:c.1361-1939G>A	N/A	Intron Variant
MAGI3 transcript variant 2	NM_152900.3:c.1361-1939G>A	N/A	Intron Variant
MAGI3 transcript variant X2	XM_005270737.4:c.1361-193… XM_005270737.4:c.1361-1939G>A	N/A	Intron Variant
MAGI3 transcript variant X1	XM_017000974.2:c.1361-193… XM_017000974.2:c.1361-1939G>A	N/A	Intron Variant
MAGI3 transcript variant X3	XM_047417371.1:c.1361-193… XM_047417371.1:c.1361-1939G>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	C	T
GRCh38.p14 chr 1	NC_000001.11:g.113639972=	NC_000001.11:g.113639972G>A	NC_000001.11:g.113639972G>C	NC_000001.11:g.113639972G>T
GRCh37.p13 chr 1	NC_000001.10:g.114182594=	NC_000001.10:g.114182594G>A	NC_000001.10:g.114182594G>C	NC_000001.10:g.114182594G>T
MAGI3 transcript variant 1	NM_001142782.1:c.1361-1939=	NM_001142782.1:c.1361-1939G>A	NM_001142782.1:c.1361-1939G>C	NM_001142782.1:c.1361-1939G>T
MAGI3 transcript variant 1	NM_001142782.2:c.1361-1939=	NM_001142782.2:c.1361-1939G>A	NM_001142782.2:c.1361-1939G>C	NM_001142782.2:c.1361-1939G>T
MAGI3 transcript variant 2	NM_152900.2:c.1361-1939=	NM_152900.2:c.1361-1939G>A	NM_152900.2:c.1361-1939G>C	NM_152900.2:c.1361-1939G>T
MAGI3 transcript variant 2	NM_152900.3:c.1361-1939=	NM_152900.3:c.1361-1939G>A	NM_152900.3:c.1361-1939G>C	NM_152900.3:c.1361-1939G>T
MAGI3 transcript variant X1	XM_005270736.1:c.1436-1939=	XM_005270736.1:c.1436-1939G>A	XM_005270736.1:c.1436-1939G>C	XM_005270736.1:c.1436-1939G>T
MAGI3 transcript variant X2	XM_005270737.1:c.1361-1939=	XM_005270737.1:c.1361-1939G>A	XM_005270737.1:c.1361-1939G>C	XM_005270737.1:c.1361-1939G>T
MAGI3 transcript variant X2	XM_005270737.4:c.1361-1939=	XM_005270737.4:c.1361-1939G>A	XM_005270737.4:c.1361-1939G>C	XM_005270737.4:c.1361-1939G>T
MAGI3 transcript variant X1	XM_017000974.2:c.1361-1939=	XM_017000974.2:c.1361-1939G>A	XM_017000974.2:c.1361-1939G>C	XM_017000974.2:c.1361-1939G>T
MAGI3 transcript variant X3	XM_047417371.1:c.1361-1939=	XM_047417371.1:c.1361-1939G>A	XM_047417371.1:c.1361-1939G>C	XM_047417371.1:c.1361-1939G>T

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#.

61 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20576281	Apr 05, 2004 (121)
2	ABI	ss41143699	Mar 15, 2006 (126)
3	BCMHGSC_JDW	ss87726874	Mar 23, 2008 (129)
4	HUMANGENOME_JCVI	ss99242220	Feb 05, 2009 (130)
5	BGI	ss106596096	Feb 05, 2009 (130)
6	ENSEMBL	ss131641498	Dec 01, 2009 (131)
7	ENSEMBL	ss138063334	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss165058029	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss167018425	Jul 04, 2010 (132)
10	BUSHMAN	ss198954335	Jul 04, 2010 (132)
11	1000GENOMES	ss210461279	Jul 14, 2010 (132)
12	1000GENOMES	ss230698455	Jul 14, 2010 (132)
13	BL	ss253396649	May 09, 2011 (134)
14	PJP	ss290602183	May 09, 2011 (134)
15	TISHKOFF	ss554594350	Apr 25, 2013 (138)
16	SSMP	ss648323689	Apr 25, 2013 (138)
17	EVA-GONL	ss975587414	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1068205553	Aug 21, 2014 (142)
19	1000GENOMES	ss1292497918	Aug 21, 2014 (142)
20	DDI	ss1425942341	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1574333905	Apr 01, 2015 (144)
22	EVA_DECODE	ss1584968277	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1601025024	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1644019057	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1794957214	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1918787736	Feb 12, 2016 (147)
27	JJLAB	ss2019918290	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2147937028	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2165848179	Dec 20, 2016 (150)
30	GRF	ss2697867360	Nov 08, 2017 (151)
31	GNOMAD	ss2759747363	Nov 08, 2017 (151)
32	SWEGEN	ss2987465612	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3023723681	Nov 08, 2017 (151)
34	CSHL	ss3343642791	Nov 08, 2017 (151)
35	URBANLAB	ss3646756323	Oct 11, 2018 (152)
36	EGCUT_WGS	ss3655554481	Jul 12, 2019 (153)
37	EVA_DECODE	ss3687563283	Jul 12, 2019 (153)
38	ACPOP	ss3727402893	Jul 12, 2019 (153)
39	EVA	ss3746692362	Jul 12, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3799695205	Jul 12, 2019 (153)
41	EVA	ss3826378607	Apr 25, 2020 (154)
42	EVA	ss3836581010	Apr 25, 2020 (154)
43	EVA	ss3841989454	Apr 25, 2020 (154)
44	SGDP_PRJ	ss3849684043	Apr 25, 2020 (154)
45	KRGDB	ss3894782353	Apr 25, 2020 (154)
46	KOGIC	ss3945281003	Apr 25, 2020 (154)
47	TOPMED	ss4464181641	Apr 25, 2021 (155)
48	TOMMO_GENOMICS	ss5145755648	Apr 25, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5243666372	Oct 12, 2022 (156)
50	EVA	ss5321288127	Oct 12, 2022 (156)
51	HUGCELL_USP	ss5444583971	Oct 12, 2022 (156)
52	HUGCELL_USP	ss5444583972	Oct 12, 2022 (156)
53	EVA	ss5506002607	Oct 12, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5516688848	Oct 12, 2022 (156)
55	SANFORD_IMAGENETICS	ss5626330905	Oct 12, 2022 (156)
56	TOMMO_GENOMICS	ss5671046562	Oct 12, 2022 (156)
57	YY_MCH	ss5800946012	Oct 12, 2022 (156)
58	EVA	ss5832506134	Oct 12, 2022 (156)
59	EVA	ss5849074562	Oct 12, 2022 (156)
60	EVA	ss5909866264	Oct 12, 2022 (156)
61	EVA	ss5938198422	Oct 12, 2022 (156)
62	1000Genomes	NC_000001.10 - 114182594	Oct 11, 2018 (152)
63	1000Genomes_30x	NC_000001.11 - 113639972	Oct 12, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114182594	Oct 11, 2018 (152)
65	Genetic variation in the Estonian population	NC_000001.10 - 114182594	Oct 11, 2018 (152)
66	The Danish reference pan genome	NC_000001.10 - 114182594	Apr 25, 2020 (154)
67	gnomAD - Genomes Submission ignored due to conflicting rows: Row 23170693 (NC_000001.11:113639971:G:A 29705/140090) Row 23170694 (NC_000001.11:113639971:G:T 23/140126)	-	Apr 25, 2021 (155)
68	gnomAD - Genomes Submission ignored due to conflicting rows: Row 23170693 (NC_000001.11:113639971:G:A 29705/140090) Row 23170694 (NC_000001.11:113639971:G:T 23/140126)	-	Apr 25, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000001.10 - 114182594	Apr 25, 2020 (154)
70	KOREAN population from KRGDB	NC_000001.10 - 114182594	Apr 25, 2020 (154)
71	Korean Genome Project	NC_000001.11 - 113639972	Apr 25, 2020 (154)
72	Northern Sweden	NC_000001.10 - 114182594	Jul 12, 2019 (153)
73	Qatari	NC_000001.10 - 114182594	Apr 25, 2020 (154)
74	SGDP_PRJ	NC_000001.10 - 114182594	Apr 25, 2020 (154)
75	Siberian	NC_000001.10 - 114182594	Apr 25, 2020 (154)
76	8.3KJPN	NC_000001.10 - 114182594	Apr 25, 2021 (155)
77	14KJPN	NC_000001.11 - 113639972	Oct 12, 2022 (156)
78	TopMed	NC_000001.11 - 113639972	Apr 25, 2021 (155)
79	UK 10K study - Twins	NC_000001.10 - 114182594	Oct 11, 2018 (152)
80	A Vietnamese Genetic Variation Database	NC_000001.10 - 114182594	Jul 12, 2019 (153)
81	ALFA	NC_000001.11 - 113639972	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
ss87726874, ss165058029, ss167018425, ss198954335, ss210461279, ss253396649, ss290602183, ss1584968277	NC_000001.9:113984116:G:A	NC_000001.11:113639971:G:A	(self)
3276146, 1812410, 1292729, 1671576, 788255, 1959747, 687758, 829666, 1701023, 453382, 3724955, 1812410, 392470, ss230698455, ss554594350, ss648323689, ss975587414, ss1068205553, ss1292497918, ss1425942341, ss1574333905, ss1601025024, ss1644019057, ss1794957214, ss1918787736, ss2019918290, ss2147937028, ss2697867360, ss2759747363, ss2987465612, ss3343642791, ss3655554481, ss3727402893, ss3746692362, ss3826378607, ss3836581010, ss3849684043, ss3894782353, ss5145755648, ss5321288127, ss5506002607, ss5626330905, ss5832506134, ss5938198422	NC_000001.10:114182593:G:A	NC_000001.11:113639971:G:A	(self)
4214783, 1659004, 4883666, 27787976, 13378487537, ss2165848179, ss3023723681, ss3646756323, ss3687563283, ss3799695205, ss3841989454, ss3945281003, ss4464181641, ss5243666372, ss5444583971, ss5516688848, ss5671046562, ss5800946012, ss5849074562, ss5909866264	NC_000001.11:113639971:G:A	NC_000001.11:113639971:G:A	(self)
ss20576281	NT_019273.16:5178541:G:A	NC_000001.11:113639971:G:A	(self)
ss41143699, ss99242220, ss106596096, ss131641498, ss138063334	NT_032977.9:84154511:G:A	NC_000001.11:113639971:G:A	(self)
13378487537	NC_000001.11:113639971:G:C	NC_000001.11:113639971:G:C	(self)
13378487537, ss2165848179, ss5444583972	NC_000001.11:113639971:G:T	NC_000001.11:113639971:G:T	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2328213190	NC_000001.10:114182593:G:T	NC_000001.11:113639971:G:T

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

No publications for rs12753351

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

rs12753351