Name: rs12753075
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.

rs12753075

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113584904 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.233840 (61895/264690, TOPMED)
T=0.237015 (32918/138886, GnomAD)
T=0.25429 (9243/36348, ALFA) (+ 16 more)
T=0.06834 (1931/28254, 14KJPN)
T=0.07148 (1198/16760, 8.3KJPN)
T=0.2181 (1397/6404, 1000G_30x)
T=0.2196 (1100/5008, 1000G)
T=0.2319 (1039/4480, Estonian)
T=0.2999 (1156/3854, ALSPAC)
T=0.2905 (1077/3708, TWINSUK)
T=0.0856 (250/2922, KOREAN)
T=0.0600 (110/1832, Korea1K)
T=0.279 (278/998, GoNL)
T=0.248 (149/600, NorthernSweden)
C=0.394 (86/218, SGDP_PRJ)
T=0.319 (69/216, Qatari)
T=0.179 (38/212, Vietnamese)
T=0.33 (13/40, GENOME_DK)
C=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	36440	C=0.74544	T=0.25456
European	Sub	21998	C=0.71293	T=0.28707
African	Sub	5882	C=0.8567	T=0.1433
African Others	Sub	198	C=0.899	T=0.101
African American	Sub	5684	C=0.8552	T=0.1448
Asian	Sub	134	C=0.858	T=0.142
East Asian	Sub	104	C=0.885	T=0.115
Other Asian	Sub	30	C=0.77	T=0.23
Latin American 1	Sub	222	C=0.752	T=0.248
Latin American 2	Sub	4712	C=0.7750	T=0.2250
South Asian	Sub	114	C=0.570	T=0.430
Other	Sub	3378	C=0.7232	T=0.2768

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	C=0.766160	T=0.233840
gnomAD - Genomes	Global	Study-wide	138886	C=0.762985	T=0.237015
gnomAD - Genomes	European	Sub	75252	C=0.71036	T=0.28964
gnomAD - Genomes	African	Sub	41600	C=0.85505	T=0.14495
gnomAD - Genomes	American	Sub	13464	C=0.75995	T=0.24005
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	C=0.6999	T=0.3001
gnomAD - Genomes	East Asian	Sub	3128	C=0.8996	T=0.1004
gnomAD - Genomes	Other	Sub	2130	C=0.7408	T=0.2592
Allele Frequency Aggregator	Total	Global	36348	C=0.74571	T=0.25429
Allele Frequency Aggregator	European	Sub	21924	C=0.71315	T=0.28685
Allele Frequency Aggregator	African	Sub	5882	C=0.8567	T=0.1433
Allele Frequency Aggregator	Latin American 2	Sub	4712	C=0.7750	T=0.2250
Allele Frequency Aggregator	Other	Sub	3360	C=0.7238	T=0.2762
Allele Frequency Aggregator	Latin American 1	Sub	222	C=0.752	T=0.248
Allele Frequency Aggregator	Asian	Sub	134	C=0.858	T=0.142
Allele Frequency Aggregator	South Asian	Sub	114	C=0.570	T=0.430
14KJPN	JAPANESE	Study-wide	28254	C=0.93166	T=0.06834
8.3KJPN	JAPANESE	Study-wide	16760	C=0.92852	T=0.07148
1000Genomes_30x	Global	Study-wide	6404	C=0.7819	T=0.2181
1000Genomes_30x	African	Sub	1786	C=0.9003	T=0.0997
1000Genomes_30x	Europe	Sub	1266	C=0.6761	T=0.3239
1000Genomes_30x	South Asian	Sub	1202	C=0.6015	T=0.3985
1000Genomes_30x	East Asian	Sub	1170	C=0.9051	T=0.0949
1000Genomes_30x	American	Sub	980	C=0.777	T=0.223
1000Genomes	Global	Study-wide	5008	C=0.7804	T=0.2196
1000Genomes	African	Sub	1322	C=0.8994	T=0.1006
1000Genomes	East Asian	Sub	1008	C=0.9067	T=0.0933
1000Genomes	Europe	Sub	1006	C=0.6740	T=0.3260
1000Genomes	South Asian	Sub	978	C=0.597	T=0.403
1000Genomes	American	Sub	694	C=0.782	T=0.218
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7681	T=0.2319
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7001	T=0.2999
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7095	T=0.2905
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9144	T=0.0856
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9400	T=0.0600
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.721	T=0.279
Northern Sweden	ACPOP	Study-wide	600	C=0.752	T=0.248
SGDP_PRJ	Global	Study-wide	218	C=0.394	T=0.606
Qatari	Global	Study-wide	216	C=0.681	T=0.319
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.821	T=0.179
The Danish reference pan genome	Danish	Study-wide	40	C=0.68	T=0.33
Siberian	Global	Study-wide	30	C=0.47	T=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.113584904C>T
GRCh37.p13 chr 1	NC_000001.10:g.114127526C>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.554-483C… NM_001142782.2:c.554-483C>T	N/A	Intron Variant
MAGI3 transcript variant 2	NM_152900.3:c.554-483C>T	N/A	Intron Variant
MAGI3 transcript variant X2	XM_005270737.4:c.554-483C… XM_005270737.4:c.554-483C>T	N/A	Intron Variant
MAGI3 transcript variant X1	XM_017000974.2:c.554-483C… XM_017000974.2:c.554-483C>T	N/A	Intron Variant
MAGI3 transcript variant X3	XM_047417371.1:c.554-483C… XM_047417371.1:c.554-483C>T	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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.113584904=	NC_000001.11:g.113584904C>T
GRCh37.p13 chr 1	NC_000001.10:g.114127526=	NC_000001.10:g.114127526C>T
MAGI3 transcript variant 1	NM_001142782.1:c.554-483=	NM_001142782.1:c.554-483C>T
MAGI3 transcript variant 1	NM_001142782.2:c.554-483=	NM_001142782.2:c.554-483C>T
MAGI3 transcript variant 2	NM_152900.2:c.554-483=	NM_152900.2:c.554-483C>T
MAGI3 transcript variant 2	NM_152900.3:c.554-483=	NM_152900.3:c.554-483C>T
MAGI3 transcript variant X1	XM_005270736.1:c.554-483=	XM_005270736.1:c.554-483C>T
MAGI3 transcript variant X2	XM_005270737.1:c.554-483=	XM_005270737.1:c.554-483C>T
MAGI3 transcript variant X2	XM_005270737.4:c.554-483=	XM_005270737.4:c.554-483C>T
MAGI3 transcript variant X1	XM_017000974.2:c.554-483=	XM_017000974.2:c.554-483C>T
MAGI3 transcript variant X3	XM_047417371.1:c.554-483=	XM_047417371.1:c.554-483C>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#.

70 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20574925	Apr 05, 2004 (121)
2	ABI	ss43819736	Mar 16, 2006 (126)
3	HUMANGENOME_JCVI	ss99242190	Feb 03, 2009 (130)
4	BGI	ss102776814	Dec 01, 2009 (131)
5	1000GENOMES	ss108536923	Jan 23, 2009 (130)
6	ENSEMBL	ss138063265	Dec 01, 2009 (131)
7	ENSEMBL	ss139272417	Dec 01, 2009 (131)
8	ILLUMINA	ss161038365	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss165057328	Jul 04, 2010 (132)
10	COMPLETE_GENOMICS	ss167018051	Jul 04, 2010 (132)
11	BUSHMAN	ss198954024	Jul 04, 2010 (132)
12	1000GENOMES	ss218605939	Jul 14, 2010 (132)
13	1000GENOMES	ss230698338	Jul 14, 2010 (132)
14	1000GENOMES	ss238354689	Jul 15, 2010 (132)
15	GMI	ss275984362	May 04, 2012 (137)
16	PJP	ss290602109	May 09, 2011 (134)
17	ILLUMINA	ss479381164	Sep 08, 2015 (146)
18	TISHKOFF	ss554594118	Apr 25, 2013 (138)
19	SSMP	ss648323458	Apr 25, 2013 (138)
20	EVA-GONL	ss975587091	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1068205353	Aug 21, 2014 (142)
22	1000GENOMES	ss1292496605	Aug 21, 2014 (142)
23	DDI	ss1425942238	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1574333738	Apr 01, 2015 (144)
25	EVA_DECODE	ss1584967953	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1601024447	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1644018480	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1794956883	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1918787375	Feb 12, 2016 (147)
30	GENOMED	ss1966845283	Jul 19, 2016 (147)
31	JJLAB	ss2019918147	Sep 14, 2016 (149)
32	ILLUMINA	ss2094846994	Dec 20, 2016 (150)
33	ILLUMINA	ss2094972199	Dec 20, 2016 (150)
34	USC_VALOUEV	ss2147936861	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2165845682	Dec 20, 2016 (150)
36	GRF	ss2697867160	Nov 08, 2017 (151)
37	AFFY	ss2985522526	Nov 08, 2017 (151)
38	SWEGEN	ss2987464937	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3023723599	Nov 08, 2017 (151)
40	CSHL	ss3343642634	Nov 08, 2017 (151)
41	ILLUMINA	ss3636022078	Oct 11, 2018 (152)
42	URBANLAB	ss3646756219	Oct 11, 2018 (152)
43	ILLUMINA	ss3651455034	Oct 11, 2018 (152)
44	ILLUMINA	ss3653643503	Oct 11, 2018 (152)
45	EGCUT_WGS	ss3655553930	Jul 12, 2019 (153)
46	EVA_DECODE	ss3687562689	Jul 12, 2019 (153)
47	ACPOP	ss3727402596	Jul 12, 2019 (153)
48	EVA	ss3746692038	Jul 12, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3799694823	Jul 12, 2019 (153)
50	EVA	ss3826378421	Apr 25, 2020 (154)
51	EVA	ss3836580906	Apr 25, 2020 (154)
52	EVA	ss3841989344	Apr 25, 2020 (154)
53	SGDP_PRJ	ss3849683382	Apr 25, 2020 (154)
54	KRGDB	ss3894781408	Apr 25, 2020 (154)
55	KOGIC	ss3945280220	Apr 25, 2020 (154)
56	GNOMAD	ss4000720448	Apr 25, 2021 (155)
57	TOPMED	ss4464168709	Apr 25, 2021 (155)
58	TOMMO_GENOMICS	ss5145753944	Apr 25, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5243665174	Oct 12, 2022 (156)
60	EVA	ss5321285982	Oct 12, 2022 (156)
61	HUGCELL_USP	ss5444583070	Oct 12, 2022 (156)
62	EVA	ss5506002416	Oct 12, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5516686955	Oct 12, 2022 (156)
64	SANFORD_IMAGENETICS	ss5626330244	Oct 12, 2022 (156)
65	TOMMO_GENOMICS	ss5671044358	Oct 12, 2022 (156)
66	YY_MCH	ss5800945725	Oct 12, 2022 (156)
67	EVA	ss5832505701	Oct 12, 2022 (156)
68	EVA	ss5849074439	Oct 12, 2022 (156)
69	EVA	ss5909865117	Oct 12, 2022 (156)
70	EVA	ss5938197839	Oct 12, 2022 (156)
71	1000Genomes	NC_000001.10 - 114127526	Oct 11, 2018 (152)
72	1000Genomes_30x	NC_000001.11 - 113584904	Oct 12, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114127526	Oct 11, 2018 (152)
74	Genetic variation in the Estonian population	NC_000001.10 - 114127526	Oct 11, 2018 (152)
75	The Danish reference pan genome	NC_000001.10 - 114127526	Apr 25, 2020 (154)
76	gnomAD - Genomes	NC_000001.11 - 113584904	Apr 25, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000001.10 - 114127526	Apr 25, 2020 (154)
78	KOREAN population from KRGDB	NC_000001.10 - 114127526	Apr 25, 2020 (154)
79	Korean Genome Project	NC_000001.11 - 113584904	Apr 25, 2020 (154)
80	Northern Sweden	NC_000001.10 - 114127526	Jul 12, 2019 (153)
81	Qatari	NC_000001.10 - 114127526	Apr 25, 2020 (154)
82	SGDP_PRJ	NC_000001.10 - 114127526	Apr 25, 2020 (154)
83	Siberian	NC_000001.10 - 114127526	Apr 25, 2020 (154)
84	8.3KJPN	NC_000001.10 - 114127526	Apr 25, 2021 (155)
85	14KJPN	NC_000001.11 - 113584904	Oct 12, 2022 (156)
86	TopMed	NC_000001.11 - 113584904	Apr 25, 2021 (155)
87	UK 10K study - Twins	NC_000001.10 - 114127526	Oct 11, 2018 (152)
88	A Vietnamese Genetic Variation Database	NC_000001.10 - 114127526	Jul 12, 2019 (153)
89	ALFA	NC_000001.11 - 113584904	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
ss108536923, ss165057328, ss167018051, ss198954024, ss275984362, ss290602109, ss1584967953, ss2094846994	NC_000001.9:113929048:C:T	NC_000001.11:113584903:C:T	(self)
3274784, 1811767, 1292178, 1671445, 787952, 1958802, 687461, 829305, 1700362, 453215, 3723251, 1811767, 392318, ss218605939, ss230698338, ss238354689, ss479381164, ss554594118, ss648323458, ss975587091, ss1068205353, ss1292496605, ss1425942238, ss1574333738, ss1601024447, ss1644018480, ss1794956883, ss1918787375, ss1966845283, ss2019918147, ss2094972199, ss2147936861, ss2697867160, ss2985522526, ss2987464937, ss3343642634, ss3636022078, ss3651455034, ss3653643503, ss3655553930, ss3727402596, ss3746692038, ss3826378421, ss3836580906, ss3849683382, ss3894781408, ss5145753944, ss5321285982, ss5506002416, ss5626330244, ss5832505701, ss5938197839	NC_000001.10:114127525:C:T	NC_000001.11:113584903:C:T	(self)
4212890, 23160192, 1658221, 4881462, 27775044, 2174410718, ss2165845682, ss3023723599, ss3646756219, ss3687562689, ss3799694823, ss3841989344, ss3945280220, ss4000720448, ss4464168709, ss5243665174, ss5444583070, ss5516686955, ss5671044358, ss5800945725, ss5849074439, ss5909865117	NC_000001.11:113584903:C:T	NC_000001.11:113584903:C:T	(self)
ss20574925	NT_019273.16:5123473:C:T	NC_000001.11:113584903:C:T	(self)
ss43819736, ss99242190, ss102776814, ss138063265, ss139272417, ss161038365	NT_032977.9:84099443:C:T	NC_000001.11:113584903:C:T	(self)

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

No publications for rs12753075

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12753075