Name: rs17274620
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.

rs17274620

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113674733 (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: A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.205950 (54513/264690, TOPMED)
T=0.210179 (29444/140090, GnomAD)
T=0.06905 (1951/28256, 14KJPN) (+ 16 more)
T=0.24092 (4551/18890, ALFA)
T=0.07172 (1202/16760, 8.3KJPN)
T=0.1922 (1231/6404, 1000G_30x)
T=0.1943 (973/5008, 1000G)
T=0.2306 (1033/4480, Estonian)
T=0.2976 (1147/3854, ALSPAC)
T=0.2888 (1071/3708, TWINSUK)
T=0.0859 (251/2922, KOREAN)
T=0.0590 (108/1832, Korea1K)
T=0.279 (278/998, GoNL)
T=0.248 (149/600, NorthernSweden)
T=0.315 (68/216, Qatari)
T=0.189 (40/212, Vietnamese)
A=0.385 (77/200, SGDP_PRJ)
T=0.33 (13/40, GENOME_DK)
A=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	18890	A=0.75908	T=0.24092
European	Sub	14286	A=0.72043	T=0.27957
African	Sub	2946	A=0.9433	T=0.0567
African Others	Sub	114	A=1.000	T=0.000
African American	Sub	2832	A=0.9410	T=0.0590
Asian	Sub	112	A=0.857	T=0.143
East Asian	Sub	86	A=0.88	T=0.12
Other Asian	Sub	26	A=0.77	T=0.23
Latin American 1	Sub	146	A=0.760	T=0.240
Latin American 2	Sub	610	A=0.780	T=0.220
South Asian	Sub	98	A=0.57	T=0.43
Other	Sub	692	A=0.764	T=0.236

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=0.794050	T=0.205950
gnomAD - Genomes	Global	Study-wide	140090	A=0.789821	T=0.210179
gnomAD - Genomes	European	Sub	75844	A=0.71096	T=0.28904
gnomAD - Genomes	African	Sub	41992	A=0.93937	T=0.06063
gnomAD - Genomes	American	Sub	13654	A=0.76805	T=0.23195
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.7014	T=0.2986
gnomAD - Genomes	East Asian	Sub	3128	A=0.9012	T=0.0988
gnomAD - Genomes	Other	Sub	2150	A=0.7637	T=0.2363
14KJPN	JAPANESE	Study-wide	28256	A=0.93095	T=0.06905
Allele Frequency Aggregator	Total	Global	18890	A=0.75908	T=0.24092
Allele Frequency Aggregator	European	Sub	14286	A=0.72043	T=0.27957
Allele Frequency Aggregator	African	Sub	2946	A=0.9433	T=0.0567
Allele Frequency Aggregator	Other	Sub	692	A=0.764	T=0.236
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.780	T=0.220
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.760	T=0.240
Allele Frequency Aggregator	Asian	Sub	112	A=0.857	T=0.143
Allele Frequency Aggregator	South Asian	Sub	98	A=0.57	T=0.43
8.3KJPN	JAPANESE	Study-wide	16760	A=0.92828	T=0.07172
1000Genomes_30x	Global	Study-wide	6404	A=0.8078	T=0.1922
1000Genomes_30x	African	Sub	1786	A=0.9922	T=0.0078
1000Genomes_30x	Europe	Sub	1266	A=0.6746	T=0.3254
1000Genomes_30x	South Asian	Sub	1202	A=0.5948	T=0.4052
1000Genomes_30x	East Asian	Sub	1170	A=0.9051	T=0.0949
1000Genomes_30x	American	Sub	980	A=0.789	T=0.211
1000Genomes	Global	Study-wide	5008	A=0.8057	T=0.1943
1000Genomes	African	Sub	1322	A=0.9909	T=0.0091
1000Genomes	East Asian	Sub	1008	A=0.9077	T=0.0923
1000Genomes	Europe	Sub	1006	A=0.6730	T=0.3270
1000Genomes	South Asian	Sub	978	A=0.593	T=0.407
1000Genomes	American	Sub	694	A=0.797	T=0.203
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7694	T=0.2306
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7024	T=0.2976
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7112	T=0.2888
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9141	T=0.0859
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9410	T=0.0590
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.721	T=0.279
Northern Sweden	ACPOP	Study-wide	600	A=0.752	T=0.248
Qatari	Global	Study-wide	216	A=0.685	T=0.315
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.811	T=0.189
SGDP_PRJ	Global	Study-wide	200	A=0.385	T=0.615
The Danish reference pan genome	Danish	Study-wide	40	A=0.68	T=0.33
Siberian	Global	Study-wide	30	A=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.113674733A>T
GRCh37.p13 chr 1	NC_000001.10:g.114217355A>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.3189+126… NM_001142782.2:c.3189+1268A>T	N/A	Intron Variant
MAGI3 transcript variant 2	NM_152900.3:c.3189+1268A>T	N/A	Intron Variant
MAGI3 transcript variant X2	XM_005270737.4:c.3189+126… XM_005270737.4:c.3189+1268A>T	N/A	Intron Variant
MAGI3 transcript variant X1	XM_017000974.2:c.3189+126… XM_017000974.2:c.3189+1268A>T	N/A	Intron Variant
MAGI3 transcript variant X3	XM_047417371.1:c.2816-646… XM_047417371.1:c.2816-6465A>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	A=	T
GRCh38.p14 chr 1	NC_000001.11:g.113674733=	NC_000001.11:g.113674733A>T
GRCh37.p13 chr 1	NC_000001.10:g.114217355=	NC_000001.10:g.114217355A>T
MAGI3 transcript variant 1	NM_001142782.1:c.3189+1268=	NM_001142782.1:c.3189+1268A>T
MAGI3 transcript variant 1	NM_001142782.2:c.3189+1268=	NM_001142782.2:c.3189+1268A>T
MAGI3 transcript variant 2	NM_152900.2:c.3189+1268=	NM_152900.2:c.3189+1268A>T
MAGI3 transcript variant 2	NM_152900.3:c.3189+1268=	NM_152900.3:c.3189+1268A>T
MAGI3 transcript variant X1	XM_005270736.1:c.3264+1268=	XM_005270736.1:c.3264+1268A>T
MAGI3 transcript variant X2	XM_005270737.1:c.3189+1268=	XM_005270737.1:c.3189+1268A>T
MAGI3 transcript variant X2	XM_005270737.4:c.3189+1268=	XM_005270737.4:c.3189+1268A>T
MAGI3 transcript variant X1	XM_017000974.2:c.3189+1268=	XM_017000974.2:c.3189+1268A>T
MAGI3 transcript variant X3	XM_047417371.1:c.2816-6465=	XM_047417371.1:c.2816-6465A>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#.

68 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24629891	Sep 20, 2004 (123)
2	ABI	ss44091430	Mar 15, 2006 (126)
3	BCMHGSC_JDW	ss87726973	Mar 23, 2008 (129)
4	HUMANGENOME_JCVI	ss99242242	Feb 04, 2009 (130)
5	BGI	ss102776840	Dec 01, 2009 (131)
6	1000GENOMES	ss108537200	Jan 23, 2009 (130)
7	ENSEMBL	ss138063365	Dec 01, 2009 (131)
8	ENSEMBL	ss143855000	Dec 01, 2009 (131)
9	ILLUMINA	ss161038507	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss165058431	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss167018733	Jul 04, 2010 (132)
12	BUSHMAN	ss198954495	Jul 04, 2010 (132)
13	1000GENOMES	ss230698514	Jul 14, 2010 (132)
14	1000GENOMES	ss238354820	Jul 15, 2010 (132)
15	BL	ss253396776	May 09, 2011 (134)
16	GMI	ss275984561	May 04, 2012 (137)
17	PJP	ss290602223	May 09, 2011 (134)
18	ILLUMINA	ss479434843	Sep 08, 2015 (146)
19	TISHKOFF	ss554594502	Apr 25, 2013 (138)
20	SSMP	ss648323802	Apr 25, 2013 (138)
21	EVA-GONL	ss975587612	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1068205667	Aug 21, 2014 (142)
23	1000GENOMES	ss1292498672	Aug 21, 2014 (142)
24	DDI	ss1425942398	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1574333984	Apr 01, 2015 (144)
26	EVA_DECODE	ss1584968465	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1601025455	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1644019488	Apr 01, 2015 (144)
29	WEILL_CORNELL_DGM	ss1918787899	Feb 12, 2016 (147)
30	GENOMED	ss1966845372	Jul 19, 2016 (147)
31	JJLAB	ss2019918370	Sep 14, 2016 (149)
32	ILLUMINA	ss2094847122	Dec 20, 2016 (150)
33	ILLUMINA	ss2094972426	Dec 20, 2016 (150)
34	USC_VALOUEV	ss2147937128	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2165849883	Dec 20, 2016 (150)
36	GRF	ss2697867463	Nov 08, 2017 (151)
37	GNOMAD	ss2759749635	Nov 08, 2017 (151)
38	SWEGEN	ss2987465923	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3023723727	Nov 08, 2017 (151)
40	CSHL	ss3343642869	Nov 08, 2017 (151)
41	ILLUMINA	ss3636022207	Oct 11, 2018 (152)
42	URBANLAB	ss3646756385	Oct 11, 2018 (152)
43	ILLUMINA	ss3651455183	Oct 11, 2018 (152)
44	EGCUT_WGS	ss3655554794	Jul 12, 2019 (153)
45	EVA_DECODE	ss3687563641	Jul 12, 2019 (153)
46	ACPOP	ss3727403050	Jul 12, 2019 (153)
47	EVA	ss3746692566	Jul 12, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3799695407	Jul 12, 2019 (153)
49	EVA	ss3826378720	Apr 25, 2020 (154)
50	EVA	ss3836581057	Apr 25, 2020 (154)
51	EVA	ss3841989503	Apr 25, 2020 (154)
52	SGDP_PRJ	ss3849684388	Apr 25, 2020 (154)
53	KRGDB	ss3894782792	Apr 25, 2020 (154)
54	KOGIC	ss3945281374	Apr 25, 2020 (154)
55	TOPMED	ss4464188885	Apr 25, 2021 (155)
56	TOMMO_GENOMICS	ss5145756518	Apr 25, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5243667021	Oct 12, 2022 (156)
58	EVA	ss5321289300	Oct 12, 2022 (156)
59	HUGCELL_USP	ss5444584576	Oct 12, 2022 (156)
60	EVA	ss5506002701	Oct 12, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5516689829	Oct 12, 2022 (156)
62	SANFORD_IMAGENETICS	ss5626331256	Oct 12, 2022 (156)
63	TOMMO_GENOMICS	ss5671047702	Oct 12, 2022 (156)
64	YY_MCH	ss5800946170	Oct 12, 2022 (156)
65	EVA	ss5832506399	Oct 12, 2022 (156)
66	EVA	ss5849074645	Oct 12, 2022 (156)
67	EVA	ss5909867041	Oct 12, 2022 (156)
68	EVA	ss5938198799	Oct 12, 2022 (156)
69	1000Genomes	NC_000001.10 - 114217355	Oct 11, 2018 (152)
70	1000Genomes_30x	NC_000001.11 - 113674733	Oct 12, 2022 (156)
71	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114217355	Oct 11, 2018 (152)
72	Genetic variation in the Estonian population	NC_000001.10 - 114217355	Oct 11, 2018 (152)
73	The Danish reference pan genome	NC_000001.10 - 114217355	Apr 25, 2020 (154)
74	gnomAD - Genomes	NC_000001.11 - 113674733	Apr 25, 2021 (155)
75	Genome of the Netherlands Release 5	NC_000001.10 - 114217355	Apr 25, 2020 (154)
76	KOREAN population from KRGDB	NC_000001.10 - 114217355	Apr 25, 2020 (154)
77	Korean Genome Project	NC_000001.11 - 113674733	Apr 25, 2020 (154)
78	Northern Sweden	NC_000001.10 - 114217355	Jul 12, 2019 (153)
79	Qatari	NC_000001.10 - 114217355	Apr 25, 2020 (154)
80	SGDP_PRJ	NC_000001.10 - 114217355	Apr 25, 2020 (154)
81	Siberian	NC_000001.10 - 114217355	Apr 25, 2020 (154)
82	8.3KJPN	NC_000001.10 - 114217355	Apr 25, 2021 (155)
83	14KJPN	NC_000001.11 - 113674733	Oct 12, 2022 (156)
84	TopMed	NC_000001.11 - 113674733	Apr 25, 2021 (155)
85	UK 10K study - Twins	NC_000001.10 - 114217355	Oct 11, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000001.10 - 114217355	Jul 12, 2019 (153)
87	ALFA	NC_000001.11 - 113674733	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
ss87726973, ss108537200, ss165058431, ss167018733, ss198954495, ss253396776, ss275984561, ss290602223, ss1584968465, ss2094847122	NC_000001.9:114018877:A:T	NC_000001.11:113674732:A:T	(self)
3276939, 1812878, 1293042, 1671645, 788448, 1960186, 687915, 829829, 1701368, 453482, 3725825, 1812878, 392563, ss230698514, ss238354820, ss479434843, ss554594502, ss648323802, ss975587612, ss1068205667, ss1292498672, ss1425942398, ss1574333984, ss1601025455, ss1644019488, ss1918787899, ss1966845372, ss2019918370, ss2094972426, ss2147937128, ss2697867463, ss2759749635, ss2987465923, ss3343642869, ss3636022207, ss3651455183, ss3655554794, ss3727403050, ss3746692566, ss3826378720, ss3836581057, ss3849684388, ss3894782792, ss5145756518, ss5321289300, ss5506002701, ss5626331256, ss5832506399, ss5938198799	NC_000001.10:114217354:A:T	NC_000001.11:113674732:A:T	(self)
4215764, 23176691, 1659375, 4884806, 27795220, 11800619460, ss2165849883, ss3023723727, ss3646756385, ss3687563641, ss3799695407, ss3841989503, ss3945281374, ss4464188885, ss5243667021, ss5444584576, ss5516689829, ss5671047702, ss5800946170, ss5849074645, ss5909867041	NC_000001.11:113674732:A:T	NC_000001.11:113674732:A:T	(self)
ss24629891, ss44091430, ss99242242, ss102776840, ss138063365, ss143855000, ss161038507	NT_032977.9:84189272:A:T	NC_000001.11:113674732:A: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 rs17274620

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

rs17274620