Name: rs4974588
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.

rs4974588

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:1292022 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.179655 (47553/264690, TOPMED)
T=0.34960 (9879/28258, 14KJPN)
T=0.35125 (5887/16760, 8.3KJPN) (+ 12 more)
T=0.02781 (463/16648, ALFA)
T=0.2694 (1725/6404, 1000G_30x)
T=0.2684 (1344/5008, 1000G)
T=0.0281 (126/4480, Estonian)
T=0.3976 (1165/2930, KOREAN)
T=0.3903 (715/1832, Korea1K)
T=0.025 (25/998, GoNL)
T=0.038 (23/600, NorthernSweden)
C=0.387 (103/266, SGDP_PRJ)
T=0.120 (26/216, Qatari)
T=0.416 (89/214, Vietnamese)
C=0.44 (7/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MAEA : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	16648	C=0.97219	G=0.00000, T=0.02781
European	Sub	13926	C=0.98521	G=0.00000, T=0.01479
African	Sub	1626	C=0.8585	G=0.0000, T=0.1415
African Others	Sub	62	C=0.76	G=0.00, T=0.24
African American	Sub	1564	C=0.8625	G=0.0000, T=0.1375
Asian	Sub	42	C=0.95	G=0.00, T=0.05
East Asian	Sub	28	C=0.93	G=0.00, T=0.07
Other Asian	Sub	14	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	120	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	306	C=1.000	G=0.000, T=0.000
South Asian	Sub	88	C=0.99	G=0.00, T=0.01
Other	Sub	540	C=0.956	G=0.000, T=0.044

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=0.820345	T=0.179655
14KJPN	JAPANESE	Study-wide	28258	C=0.65040	T=0.34960
8.3KJPN	JAPANESE	Study-wide	16760	C=0.64875	T=0.35125
Allele Frequency Aggregator	Total	Global	16648	C=0.97219	G=0.00000, T=0.02781
Allele Frequency Aggregator	European	Sub	13926	C=0.98521	G=0.00000, T=0.01479
Allele Frequency Aggregator	African	Sub	1626	C=0.8585	G=0.0000, T=0.1415
Allele Frequency Aggregator	Other	Sub	540	C=0.956	G=0.000, T=0.044
Allele Frequency Aggregator	Latin American 2	Sub	306	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	120	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	88	C=0.99	G=0.00, T=0.01
Allele Frequency Aggregator	Asian	Sub	42	C=0.95	G=0.00, T=0.05
1000Genomes_30x	Global	Study-wide	6404	C=0.7294	G=0.0012, T=0.2694
1000Genomes_30x	African	Sub	1786	C=0.6193	G=0.0000, T=0.3807
1000Genomes_30x	Europe	Sub	1266	C=0.9668	G=0.0000, T=0.0332
1000Genomes_30x	South Asian	Sub	1202	C=0.8220	G=0.0067, T=0.1714
1000Genomes_30x	East Asian	Sub	1170	C=0.5718	G=0.0000, T=0.4282
1000Genomes_30x	American	Sub	980	C=0.698	G=0.000, T=0.302
1000Genomes	Global	Study-wide	5008	C=0.7302	G=0.0014, T=0.2684
1000Genomes	African	Sub	1322	C=0.6082	G=0.0000, T=0.3918
1000Genomes	East Asian	Sub	1008	C=0.5774	G=0.0000, T=0.4226
1000Genomes	Europe	Sub	1006	C=0.9712	G=0.0000, T=0.0288
1000Genomes	South Asian	Sub	978	C=0.825	G=0.007, T=0.168
1000Genomes	American	Sub	694	C=0.702	G=0.000, T=0.298
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9719	T=0.0281
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6024	T=0.3976
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6097	T=0.3903
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.975	T=0.025
Northern Sweden	ACPOP	Study-wide	600	C=0.962	T=0.038
SGDP_PRJ	Global	Study-wide	266	C=0.387	G=0.004, T=0.609
Qatari	Global	Study-wide	216	C=0.880	T=0.120
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.584	T=0.416
Siberian	Global	Study-wide	16	C=0.44	T=0.56

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 4	NC_000004.12:g.1292022C>G
GRCh38.p14 chr 4	NC_000004.12:g.1292022C>T
GRCh37.p13 chr 4	NC_000004.11:g.1285810C>G
GRCh37.p13 chr 4	NC_000004.11:g.1285810C>T

Gene: MAEA, macrophage erythroblast attacher, E3 ubiquitin ligase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAEA transcript variant 1	NM_001017405.3:c.69+2040C… NM_001017405.3:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant 3	NM_001297430.2:c.69+2040C… NM_001297430.2:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant 4	NM_001297431.2:c.69+2040C… NM_001297431.2:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant 2	NM_005882.5:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant 5	NM_001297432.2:c.	N/A	Genic Upstream Transcript Variant
MAEA transcript variant 6	NM_001297433.2:c.	N/A	Genic Upstream Transcript Variant
MAEA transcript variant 7	NR_123716.2:n.	N/A	Intron Variant
MAEA transcript variant X1	XM_006713849.3:c.69+2040C… XM_006713849.3:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant X4	XM_047449494.1:c.69+2040C… XM_047449494.1:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant X5	XM_047449495.1:c.69+2040C… XM_047449495.1:c.69+2040C>G	N/A	Intron Variant
MAEA transcript variant X2	XM_006713850.3:c.	N/A	Genic Upstream Transcript Variant
MAEA transcript variant X3	XM_047449493.1:c.	N/A	Genic Upstream 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	C=	G	T
GRCh38.p14 chr 4	NC_000004.12:g.1292022=	NC_000004.12:g.1292022C>G	NC_000004.12:g.1292022C>T
GRCh37.p13 chr 4	NC_000004.11:g.1285810=	NC_000004.11:g.1285810C>G	NC_000004.11:g.1285810C>T
MAEA transcript variant 1	NM_001017405.1:c.69+2040=	NM_001017405.1:c.69+2040C>G	NM_001017405.1:c.69+2040C>T
MAEA transcript variant 1	NM_001017405.3:c.69+2040=	NM_001017405.3:c.69+2040C>G	NM_001017405.3:c.69+2040C>T
MAEA transcript variant 3	NM_001297430.2:c.69+2040=	NM_001297430.2:c.69+2040C>G	NM_001297430.2:c.69+2040C>T
MAEA transcript variant 4	NM_001297431.2:c.69+2040=	NM_001297431.2:c.69+2040C>G	NM_001297431.2:c.69+2040C>T
MAEA transcript variant 2	NM_005882.3:c.69+2040=	NM_005882.3:c.69+2040C>G	NM_005882.3:c.69+2040C>T
MAEA transcript variant 2	NM_005882.5:c.69+2040=	NM_005882.5:c.69+2040C>G	NM_005882.5:c.69+2040C>T
MAEA transcript variant X3	XM_005272245.1:c.69+2040=	XM_005272245.1:c.69+2040C>G	XM_005272245.1:c.69+2040C>T
MAEA transcript variant X4	XM_005272246.1:c.69+2040=	XM_005272246.1:c.69+2040C>G	XM_005272246.1:c.69+2040C>T
MAEA transcript variant X5	XM_005272247.1:c.69+2040=	XM_005272247.1:c.69+2040C>G	XM_005272247.1:c.69+2040C>T
MAEA transcript variant X6	XM_005272248.1:c.69+2040=	XM_005272248.1:c.69+2040C>G	XM_005272248.1:c.69+2040C>T
MAEA transcript variant X7	XM_005272249.1:c.69+2040=	XM_005272249.1:c.69+2040C>G	XM_005272249.1:c.69+2040C>T
MAEA transcript variant X1	XM_006713849.3:c.69+2040=	XM_006713849.3:c.69+2040C>G	XM_006713849.3:c.69+2040C>T
MAEA transcript variant X4	XM_047449494.1:c.69+2040=	XM_047449494.1:c.69+2040C>G	XM_047449494.1:c.69+2040C>T
MAEA transcript variant X5	XM_047449495.1:c.69+2040=	XM_047449495.1:c.69+2040C>G	XM_047449495.1:c.69+2040C>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#.

55 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6885789	Feb 20, 2003 (111)
2	ABI	ss42202884	Mar 14, 2006 (126)
3	HGSV	ss81353626	Dec 14, 2007 (130)
4	BGI	ss104032015	Dec 01, 2009 (131)
5	1000GENOMES	ss111653221	Jan 25, 2009 (130)
6	ILLUMINA-UK	ss116836344	Feb 14, 2009 (130)
7	ENSEMBL	ss161494411	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss162992726	Jul 04, 2010 (132)
9	1000GENOMES	ss220691895	Jul 14, 2010 (132)
10	1000GENOMES	ss239553316	Jul 15, 2010 (132)
11	GMI	ss277538328	May 04, 2012 (137)
12	TISHKOFF	ss557251954	Apr 25, 2013 (138)
13	SSMP	ss651005286	Apr 25, 2013 (138)
14	EVA-GONL	ss979669972	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1071213244	Aug 21, 2014 (142)
16	1000GENOMES	ss1308076194	Aug 21, 2014 (142)
17	1000GENOMES	ss1308076195	Aug 21, 2014 (142)
18	EVA_DECODE	ss1589166386	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1609230371	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1609230372	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1652224404	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1652224405	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1800788003	Sep 08, 2015 (146)
24	WEILL_CORNELL_DGM	ss1922900541	Feb 12, 2016 (147)
25	GENOMED	ss1969636852	Jul 19, 2016 (147)
26	JJLAB	ss2022024106	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2150129954	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2259798601	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2625513042	Nov 08, 2017 (151)
30	GRF	ss2705564370	Nov 08, 2017 (151)
31	GNOMAD	ss2804653360	Nov 08, 2017 (151)
32	SWEGEN	ss2993987640	Nov 08, 2017 (151)
33	CSHL	ss3345496922	Nov 08, 2017 (151)
34	EGCUT_WGS	ss3661925979	Jul 13, 2019 (153)
35	EVA_DECODE	ss3711230136	Jul 13, 2019 (153)
36	EVA_DECODE	ss3711230137	Jul 13, 2019 (153)
37	ACPOP	ss3730775500	Jul 13, 2019 (153)
38	EVA	ss3761280922	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3804420728	Jul 13, 2019 (153)
40	EVA	ss3828324485	Apr 25, 2020 (154)
41	SGDP_PRJ	ss3858016175	Apr 25, 2020 (154)
42	KRGDB	ss3904142496	Apr 25, 2020 (154)
43	KOGIC	ss3953346459	Apr 25, 2020 (154)
44	TOPMED	ss4600073684	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5163803271	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5257731167	Oct 13, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5257731168	Oct 13, 2022 (156)
48	HUGCELL_USP	ss5456686771	Oct 13, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5538024499	Oct 13, 2022 (156)
50	SANFORD_IMAGENETICS	ss5634167472	Oct 13, 2022 (156)
51	TOMMO_GENOMICS	ss5697333420	Oct 13, 2022 (156)
52	YY_MCH	ss5804674770	Oct 13, 2022 (156)
53	EVA	ss5843424278	Oct 13, 2022 (156)
54	EVA	ss5854045087	Oct 13, 2022 (156)
55	EVA	ss5962543010	Oct 13, 2022 (156)
56	1000Genomes	NC_000004.11 - 1285810	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000004.12 - 1292022	Oct 13, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 10821922 (NC_000004.11:1285809:C:C 3734/3854, NC_000004.11:1285809:C:T 120/3854) Row 10821923 (NC_000004.11:1285809:C:C 3853/3854, NC_000004.11:1285809:C:G 1/3854)	-	Oct 12, 2018 (152)
59	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 10821922 (NC_000004.11:1285809:C:C 3734/3854, NC_000004.11:1285809:C:T 120/3854) Row 10821923 (NC_000004.11:1285809:C:C 3853/3854, NC_000004.11:1285809:C:G 1/3854)	-	Oct 12, 2018 (152)
60	Genetic variation in the Estonian population	NC_000004.11 - 1285810	Oct 12, 2018 (152)
61	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137820834 (NC_000004.12:1292021:C:G 0/140112) Row 137820835 (NC_000004.12:1292021:C:T 21414/140070)	-	Apr 26, 2021 (155)
62	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137820834 (NC_000004.12:1292021:C:G 0/140112) Row 137820835 (NC_000004.12:1292021:C:T 21414/140070)	-	Apr 26, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000004.11 - 1285810	Apr 25, 2020 (154)
64	KOREAN population from KRGDB	NC_000004.11 - 1285810	Apr 25, 2020 (154)
65	Korean Genome Project	NC_000004.12 - 1292022	Apr 25, 2020 (154)
66	Northern Sweden	NC_000004.11 - 1285810	Jul 13, 2019 (153)
67	Qatari	NC_000004.11 - 1285810	Apr 25, 2020 (154)
68	SGDP_PRJ	NC_000004.11 - 1285810	Apr 25, 2020 (154)
69	Siberian	NC_000004.11 - 1285810	Apr 25, 2020 (154)
70	8.3KJPN	NC_000004.11 - 1285810	Apr 26, 2021 (155)
71	14KJPN	NC_000004.12 - 1292022	Oct 13, 2022 (156)
72	TopMed	NC_000004.12 - 1292022	Apr 26, 2021 (155)
73	UK 10K study - Twins Submission ignored due to conflicting rows: Row 10821922 (NC_000004.11:1285809:C:C 3608/3708, NC_000004.11:1285809:C:T 100/3708) Row 10821923 (NC_000004.11:1285809:C:C 3708/3708, NC_000004.11:1285809:C:G 0/3708)	-	Oct 12, 2018 (152)
74	UK 10K study - Twins Submission ignored due to conflicting rows: Row 10821922 (NC_000004.11:1285809:C:C 3608/3708, NC_000004.11:1285809:C:T 100/3708) Row 10821923 (NC_000004.11:1285809:C:C 3708/3708, NC_000004.11:1285809:C:G 0/3708)	-	Oct 12, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000004.11 - 1285810	Jul 13, 2019 (153)
76	ALFA	NC_000004.12 - 1292022	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)
rs57521496	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
19413736, 10033155, ss1308076194, ss1609230372, ss1652224405, ss2804653360, ss3858016175, ss5634167472	NC_000004.11:1285809:C:G	NC_000004.12:1292021:C:G	(self)
25550434, 15487872557, ss3711230136, ss5257731168, ss5538024499	NC_000004.12:1292021:C:G	NC_000004.12:1292021:C:G	(self)
ss81353626	NC_000004.9:1275639:C:T	NC_000004.12:1292021:C:T	(self)
ss111653221, ss116836344, ss162992726, ss277538328, ss1589166386	NC_000004.10:1275809:C:T	NC_000004.12:1292021:C:T	(self)
19413736, 7664227, 4756664, 11319890, 4060365, 4942471, 10033155, 2646308, 21772578, 2366215, ss220691895, ss239553316, ss557251954, ss651005286, ss979669972, ss1071213244, ss1308076195, ss1609230371, ss1652224404, ss1800788003, ss1922900541, ss1969636852, ss2022024106, ss2150129954, ss2625513042, ss2705564370, ss2804653360, ss2993987640, ss3345496922, ss3661925979, ss3730775500, ss3761280922, ss3828324485, ss3858016175, ss3904142496, ss5163803271, ss5634167472, ss5843424278, ss5962543010	NC_000004.11:1285809:C:T	NC_000004.12:1292021:C:T	(self)
25550434, 9724460, 31170524, 437451240, 15487872557, ss2259798601, ss3711230137, ss3804420728, ss3953346459, ss4600073684, ss5257731167, ss5456686771, ss5538024499, ss5697333420, ss5804674770, ss5854045087	NC_000004.12:1292021:C:T	NC_000004.12:1292021:C:T	(self)
ss6885789, ss42202884, ss104032015, ss161494411	NT_037622.5:1275809:C:T	NC_000004.12:1292021: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 rs4974588

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

rs4974588