Name: rs4714087
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.

rs4714087

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:37635327 (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=0.394507 (104422/264690, TOPMED)
A=0.410259 (57360/139814, GnomAD)
A=0.45755 (13968/30528, ALFA) (+ 14 more)
G=0.43014 (12155/28258, 14KJPN)
G=0.43085 (7221/16760, 8.3KJPN)
A=0.4160 (2664/6404, 1000G_30x)
A=0.4201 (2104/5008, 1000G)
G=0.4799 (2149/4478, Estonian)
A=0.4935 (1902/3854, ALSPAC)
A=0.4954 (1837/3708, TWINSUK)
G=0.3648 (1068/2928, KOREAN)
A=0.451 (450/998, GoNL)
G=0.458 (275/600, NorthernSweden)
G=0.342 (113/330, SGDP_PRJ)
A=0.310 (67/216, Qatari)
G=0.30 (15/50, Siberian)
A=0.42 (17/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MDGA1 : 3 Prime UTR 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	30528	G=0.54245	A=0.45755
European	Sub	24476	G=0.50915	A=0.49085
African	Sub	3138	G=0.7588	A=0.2412
African Others	Sub	124	G=0.831	A=0.169
African American	Sub	3014	G=0.7558	A=0.2442
Asian	Sub	126	G=0.317	A=0.683
East Asian	Sub	98	G=0.32	A=0.68
Other Asian	Sub	28	G=0.32	A=0.68
Latin American 1	Sub	164	G=0.652	A=0.348
Latin American 2	Sub	684	G=0.602	A=0.398
South Asian	Sub	114	G=0.553	A=0.447
Other	Sub	1826	G=0.5997	A=0.4003

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=0.605493	A=0.394507
gnomAD - Genomes	Global	Study-wide	139814	G=0.589741	A=0.410259
gnomAD - Genomes	European	Sub	75660	G=0.50131	A=0.49869
gnomAD - Genomes	African	Sub	41928	G=0.75188	A=0.24812
gnomAD - Genomes	American	Sub	13640	G=0.60279	A=0.39721
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.6724	A=0.3276
gnomAD - Genomes	East Asian	Sub	3116	G=0.3890	A=0.6110
gnomAD - Genomes	Other	Sub	2152	G=0.6204	A=0.3796
Allele Frequency Aggregator	Total	Global	30528	G=0.54245	A=0.45755
Allele Frequency Aggregator	European	Sub	24476	G=0.50915	A=0.49085
Allele Frequency Aggregator	African	Sub	3138	G=0.7588	A=0.2412
Allele Frequency Aggregator	Other	Sub	1826	G=0.5997	A=0.4003
Allele Frequency Aggregator	Latin American 2	Sub	684	G=0.602	A=0.398
Allele Frequency Aggregator	Latin American 1	Sub	164	G=0.652	A=0.348
Allele Frequency Aggregator	Asian	Sub	126	G=0.317	A=0.683
Allele Frequency Aggregator	South Asian	Sub	114	G=0.553	A=0.447
14KJPN	JAPANESE	Study-wide	28258	G=0.43014	A=0.56986
8.3KJPN	JAPANESE	Study-wide	16760	G=0.43085	A=0.56915
1000Genomes_30x	Global	Study-wide	6404	G=0.5840	A=0.4160
1000Genomes_30x	African	Sub	1786	G=0.8001	A=0.1999
1000Genomes_30x	Europe	Sub	1266	G=0.5087	A=0.4913
1000Genomes_30x	South Asian	Sub	1202	G=0.5433	A=0.4567
1000Genomes_30x	East Asian	Sub	1170	G=0.3906	A=0.6094
1000Genomes_30x	American	Sub	980	G=0.568	A=0.432
1000Genomes	Global	Study-wide	5008	G=0.5799	A=0.4201
1000Genomes	African	Sub	1322	G=0.7950	A=0.2050
1000Genomes	East Asian	Sub	1008	G=0.4028	A=0.5972
1000Genomes	Europe	Sub	1006	G=0.5129	A=0.4871
1000Genomes	South Asian	Sub	978	G=0.549	A=0.451
1000Genomes	American	Sub	694	G=0.568	A=0.432
Genetic variation in the Estonian population	Estonian	Study-wide	4478	G=0.4799	A=0.5201
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.5065	A=0.4935
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.5046	A=0.4954
KOREAN population from KRGDB	KOREAN	Study-wide	2928	G=0.3648	A=0.6352
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.549	A=0.451
Northern Sweden	ACPOP	Study-wide	600	G=0.458	A=0.542
SGDP_PRJ	Global	Study-wide	330	G=0.342	A=0.658
Qatari	Global	Study-wide	216	G=0.690	A=0.310
Siberian	Global	Study-wide	50	G=0.30	A=0.70
The Danish reference pan genome	Danish	Study-wide	40	G=0.57	A=0.42

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 6	NC_000006.12:g.37635327G>A
GRCh37.p13 chr 6	NC_000006.11:g.37603103G>A
MDGA1 RefSeqGene	NG_051764.1:g.67664C>T

Gene: MDGA1, MAM domain containing glycosylphosphatidylinositol anchor 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MDGA1 transcript	NM_153487.4:c.*2041=	N/A	3 Prime UTR Variant
MDGA1 transcript variant X2	XM_017010734.2:c.*2041=	N/A	3 Prime UTR Variant
MDGA1 transcript variant X1	XM_006715056.4:c.	N/A	Genic Downstream Transcript Variant
MDGA1 transcript variant X3	XM_047418637.1:c.	N/A	Genic Downstream Transcript Variant
MDGA1 transcript variant X5	XM_047418638.1:c.	N/A	Genic Downstream Transcript Variant
MDGA1 transcript variant X4	XR_926141.3:n.	N/A	Genic Downstream Transcript 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 6	NC_000006.12:g.37635327=	NC_000006.12:g.37635327G>A
GRCh37.p13 chr 6	NC_000006.11:g.37603103=	NC_000006.11:g.37603103G>A
MDGA1 RefSeqGene	NG_051764.1:g.67664=	NG_051764.1:g.67664C>T
MDGA1 transcript	NM_153487.4:c.*2041=	NM_153487.4:c.*2041C>T
MDGA1 transcript	NM_153487.3:c.*2041=	NM_153487.3:c.*2041C>T
MDGA1 transcript variant X2	XM_017010734.2:c.*2041=	XM_017010734.2:c.*2041C>T
MDGA1 transcript variant X2	XM_017010734.1:c.*2041=	XM_017010734.1:c.*2041C>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#.

66 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6496164	Feb 20, 2003 (111)
2	CSHL-HAPMAP	ss20263094	Feb 27, 2004 (120)
3	SI_EXO	ss69378079	May 17, 2007 (127)
4	HGSV	ss80339009	Dec 14, 2007 (130)
5	ILLUMINA-UK	ss116424036	Feb 14, 2009 (130)
6	GMI	ss156816239	Dec 01, 2009 (131)
7	1000GENOMES	ss210645188	Jul 14, 2010 (132)
8	1000GENOMES	ss222339933	Jul 14, 2010 (132)
9	1000GENOMES	ss233433322	Jul 14, 2010 (132)
10	1000GENOMES	ss240498065	Jul 15, 2010 (132)
11	BL	ss254251873	May 09, 2011 (134)
12	GMI	ss278758326	May 04, 2012 (137)
13	PJP	ss293839516	May 09, 2011 (134)
14	ILLUMINA	ss479153170	May 04, 2012 (137)
15	ILLUMINA	ss485236818	May 04, 2012 (137)
16	ILLUMINA	ss532749699	Sep 08, 2015 (146)
17	SSMP	ss653083242	Apr 25, 2013 (138)
18	ILLUMINA	ss779068071	Sep 08, 2015 (146)
19	ILLUMINA	ss780910180	Sep 08, 2015 (146)
20	ILLUMINA	ss834531480	Sep 08, 2015 (146)
21	EVA-GONL	ss982829343	Aug 21, 2014 (142)
22	1000GENOMES	ss1319741765	Aug 21, 2014 (142)
23	DDI	ss1430691871	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1581632730	Apr 01, 2015 (144)
25	EVA_DECODE	ss1592363381	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1615370332	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1658364365	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1926086556	Feb 12, 2016 (147)
29	GENOMED	ss1970373959	Jul 19, 2016 (147)
30	JJLAB	ss2023680787	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2151858282	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2283279885	Dec 20, 2016 (150)
33	ILLUMINA	ss2634440835	Nov 08, 2017 (151)
34	GRF	ss2707455674	Nov 08, 2017 (151)
35	GNOMAD	ss2837913051	Nov 08, 2017 (151)
36	SWEGEN	ss2998909096	Nov 08, 2017 (151)
37	CSHL	ss3346917390	Nov 08, 2017 (151)
38	ILLUMINA	ss3629525722	Oct 12, 2018 (152)
39	ILLUMINA	ss3632358184	Oct 12, 2018 (152)
40	URBANLAB	ss3648330807	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3666796680	Jul 13, 2019 (153)
42	EVA_DECODE	ss3717019472	Jul 13, 2019 (153)
43	ACPOP	ss3733419093	Jul 13, 2019 (153)
44	EVA	ss3764900570	Jul 13, 2019 (153)
45	KHV_HUMAN_GENOMES	ss3808051663	Jul 13, 2019 (153)
46	EVA	ss3829873650	Apr 26, 2020 (154)
47	EVA	ss3838413848	Apr 26, 2020 (154)
48	EVA	ss3843858027	Apr 26, 2020 (154)
49	SGDP_PRJ	ss3864382365	Apr 26, 2020 (154)
50	KRGDB	ss3911172405	Apr 26, 2020 (154)
51	FSA-LAB	ss3984336140	Apr 26, 2021 (155)
52	EVA	ss3986035684	Apr 26, 2021 (155)
53	TOPMED	ss4699696204	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5177073800	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5268106347	Oct 13, 2022 (156)
56	EVA	ss5365004073	Oct 13, 2022 (156)
57	HUGCELL_USP	ss5465811634	Oct 13, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5553834707	Oct 13, 2022 (156)
59	SANFORD_IMAGENETICS	ss5640208062	Oct 13, 2022 (156)
60	TOMMO_GENOMICS	ss5714995101	Oct 13, 2022 (156)
61	YY_MCH	ss5807383994	Oct 13, 2022 (156)
62	EVA	ss5842107815	Oct 13, 2022 (156)
63	EVA	ss5855316713	Oct 13, 2022 (156)
64	EVA	ss5883424019	Oct 13, 2022 (156)
65	EVA	ss5968698820	Oct 13, 2022 (156)
66	EVA	ss5980363567	Oct 13, 2022 (156)
67	1000Genomes	NC_000006.11 - 37603103	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000006.12 - 37635327	Oct 13, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 37603103	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000006.11 - 37603103	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000006.11 - 37603103	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000006.12 - 37635327	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000006.11 - 37603103	Apr 26, 2020 (154)
74	KOREAN population from KRGDB	NC_000006.11 - 37603103	Apr 26, 2020 (154)
75	Northern Sweden	NC_000006.11 - 37603103	Jul 13, 2019 (153)
76	Qatari	NC_000006.11 - 37603103	Apr 26, 2020 (154)
77	SGDP_PRJ	NC_000006.11 - 37603103	Apr 26, 2020 (154)
78	Siberian	NC_000006.11 - 37603103	Apr 26, 2020 (154)
79	8.3KJPN	NC_000006.11 - 37603103	Apr 26, 2021 (155)
80	14KJPN	NC_000006.12 - 37635327	Oct 13, 2022 (156)
81	TopMed	NC_000006.12 - 37635327	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000006.11 - 37603103	Oct 12, 2018 (152)
83	ALFA	NC_000006.12 - 37635327	Apr 26, 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).

Associated ID	History Updated (Build)
rs57785564	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80339009	NC_000006.9:37711080:G:A	NC_000006.12:37635326:G:A	(self)
ss116424036, ss210645188, ss254251873, ss278758326, ss293839516, ss485236818, ss1592363381	NC_000006.10:37711080:G:A	NC_000006.12:37635326:G:A	(self)
31516382, 17570545, 12534928, 7797669, 7821747, 18349799, 6703958, 8128486, 16399345, 4374636, 35043107, 17570545, ss222339933, ss233433322, ss240498065, ss479153170, ss532749699, ss653083242, ss779068071, ss780910180, ss834531480, ss982829343, ss1319741765, ss1430691871, ss1581632730, ss1615370332, ss1658364365, ss1926086556, ss1970373959, ss2023680787, ss2151858282, ss2634440835, ss2707455674, ss2837913051, ss2998909096, ss3346917390, ss3629525722, ss3632358184, ss3666796680, ss3733419093, ss3764900570, ss3829873650, ss3838413848, ss3864382365, ss3911172405, ss3984336140, ss3986035684, ss5177073800, ss5365004073, ss5640208062, ss5842107815, ss5968698820, ss5980363567	NC_000006.11:37603102:G:A	NC_000006.12:37635326:G:A	(self)
41360642, 222418882, 48832205, 537073762, 984450588, ss2283279885, ss3648330807, ss3717019472, ss3808051663, ss3843858027, ss4699696204, ss5268106347, ss5465811634, ss5553834707, ss5714995101, ss5807383994, ss5855316713, ss5883424019	NC_000006.12:37635326:G:A	NC_000006.12:37635326:G:A	(self)
ss20263094	NT_007592.13:28400229:G:A	NC_000006.12:37635326:G:A	(self)
ss6496164, ss69378079, ss156816239	NT_007592.15:37543102:G:A	NC_000006.12:37635326:G:A	(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 rs4714087

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

rs4714087