Name: rs4502400
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.

rs4502400

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:241072447 (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=0.082935 (21952/264690, TOPMED)
A=0.085284 (11956/140190, GnomAD)
A=0.22866 (6461/28256, 14KJPN) (+ 14 more)
A=0.09619 (1817/18890, ALFA)
A=0.23121 (3875/16760, 8.3KJPN)
A=0.0931 (596/6404, 1000G_30x)
A=0.0948 (475/5008, 1000G)
A=0.1096 (491/4480, Estonian)
A=0.2177 (638/2930, KOREAN)
A=0.092 (92/998, GoNL)
A=0.143 (86/600, NorthernSweden)
A=0.083 (18/216, Qatari)
A=0.150 (32/214, Vietnamese)
G=0.461 (59/128, SGDP_PRJ)
A=0.10 (4/40, GENOME_DK)
G=0.50 (10/20, Siberian)
A=0.50 (10/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MTERF4 : Non Coding Transcript Variant
SNED1 : 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	18890	G=0.90381	A=0.09619
European	Sub	14286	G=0.88996	A=0.11004
African	Sub	2946	G=0.9728	A=0.0272
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2832	G=0.9718	A=0.0282
Asian	Sub	112	G=0.857	A=0.143
East Asian	Sub	86	G=0.81	A=0.19
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.904	A=0.096
Latin American 2	Sub	610	G=0.902	A=0.098
South Asian	Sub	98	G=0.92	A=0.08
Other	Sub	692	G=0.903	A=0.097

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	G=0.917065	A=0.082935
gnomAD - Genomes	Global	Study-wide	140190	G=0.914716	A=0.085284
gnomAD - Genomes	European	Sub	75896	G=0.89007	A=0.10993
gnomAD - Genomes	African	Sub	42034	G=0.97033	A=0.02967
gnomAD - Genomes	American	Sub	13658	G=0.91683	A=0.08317
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.8607	A=0.1393
gnomAD - Genomes	East Asian	Sub	3128	G=0.8117	A=0.1883
gnomAD - Genomes	Other	Sub	2150	G=0.9172	A=0.0828
14KJPN	JAPANESE	Study-wide	28256	G=0.77134	A=0.22866
Allele Frequency Aggregator	Total	Global	18890	G=0.90381	A=0.09619
Allele Frequency Aggregator	European	Sub	14286	G=0.88996	A=0.11004
Allele Frequency Aggregator	African	Sub	2946	G=0.9728	A=0.0272
Allele Frequency Aggregator	Other	Sub	692	G=0.903	A=0.097
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.902	A=0.098
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.904	A=0.096
Allele Frequency Aggregator	Asian	Sub	112	G=0.857	A=0.143
Allele Frequency Aggregator	South Asian	Sub	98	G=0.92	A=0.08
8.3KJPN	JAPANESE	Study-wide	16760	G=0.76879	A=0.23121
1000Genomes_30x	Global	Study-wide	6404	G=0.9069	A=0.0931
1000Genomes_30x	African	Sub	1786	G=0.9860	A=0.0140
1000Genomes_30x	Europe	Sub	1266	G=0.8602	A=0.1398
1000Genomes_30x	South Asian	Sub	1202	G=0.9151	A=0.0849
1000Genomes_30x	East Asian	Sub	1170	G=0.8239	A=0.1761
1000Genomes_30x	American	Sub	980	G=0.912	A=0.088
1000Genomes	Global	Study-wide	5008	G=0.9052	A=0.0948
1000Genomes	African	Sub	1322	G=0.9849	A=0.0151
1000Genomes	East Asian	Sub	1008	G=0.8234	A=0.1766
1000Genomes	Europe	Sub	1006	G=0.8658	A=0.1342
1000Genomes	South Asian	Sub	978	G=0.917	A=0.083
1000Genomes	American	Sub	694	G=0.912	A=0.088
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8904	A=0.1096
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.7823	A=0.2177
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.908	A=0.092
Northern Sweden	ACPOP	Study-wide	600	G=0.857	A=0.143
Qatari	Global	Study-wide	216	G=0.917	A=0.083
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.850	A=0.150
SGDP_PRJ	Global	Study-wide	128	G=0.461	A=0.539
The Danish reference pan genome	Danish	Study-wide	40	G=0.90	A=0.10
Siberian	Global	Study-wide	20	G=0.50	A=0.50

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 2	NC_000002.12:g.241072447G>A
GRCh37.p13 chr 2	NC_000002.11:g.242011862G>A

Gene: SNED1, sushi, nidogen and EGF like domains 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNED1 transcript	NM_001080437.3:c.3817+569… NM_001080437.3:c.3817+569G>A	N/A	Intron Variant
SNED1 transcript variant X2	XM_011510931.3:c.3889+569… XM_011510931.3:c.3889+569G>A	N/A	Intron Variant
SNED1 transcript variant X7	XM_011510932.3:c.3889+569… XM_011510932.3:c.3889+569G>A	N/A	Intron Variant
SNED1 transcript variant X15	XM_011510934.4:c.3890-324… XM_011510934.4:c.3890-324G>A	N/A	Intron Variant
SNED1 transcript variant X13	XM_024452784.2:c.3889+569… XM_024452784.2:c.3889+569G>A	N/A	Intron Variant
SNED1 transcript variant X3	XM_047443884.1:c.3889+569… XM_047443884.1:c.3889+569G>A	N/A	Intron Variant
SNED1 transcript variant X8	XM_047443885.1:c.3775+569… XM_047443885.1:c.3775+569G>A	N/A	Intron Variant
SNED1 transcript variant X10	XM_047443886.1:c.3817+569… XM_047443886.1:c.3817+569G>A	N/A	Intron Variant
SNED1 transcript variant X11	XM_047443887.1:c.3703+569… XM_047443887.1:c.3703+569G>A	N/A	Intron Variant
SNED1 transcript variant X12	XM_047443888.1:c.3775+569… XM_047443888.1:c.3775+569G>A	N/A	Intron Variant
SNED1 transcript variant X14	XM_047443889.1:c.3703+569… XM_047443889.1:c.3703+569G>A	N/A	Intron Variant
SNED1 transcript variant X19	XM_047443890.1:c.48+569G… XM_047443890.1:c.48+569G>A	N/A	Intron Variant
SNED1 transcript variant X20	XM_047443891.1:c.48+569G… XM_047443891.1:c.48+569G>A	N/A	Intron Variant
SNED1 transcript variant X22	XM_011510937.3:c.	N/A	Genic Downstream Transcript Variant
SNED1 transcript variant X1	XR_002959254.2:n.	N/A	Intron Variant
SNED1 transcript variant X4	XR_002959255.2:n.	N/A	Intron Variant
SNED1 transcript variant X5	XR_002959256.2:n.	N/A	Intron Variant
SNED1 transcript variant X6	XR_002959257.2:n.	N/A	Intron Variant
SNED1 transcript variant X9	XR_002959258.2:n.	N/A	Intron Variant
SNED1 transcript variant X18	XR_002959260.2:n.	N/A	Intron Variant
SNED1 transcript variant X16	XR_002959262.2:n.	N/A	Intron Variant
SNED1 transcript variant X21	XR_002959263.2:n.	N/A	Intron Variant
SNED1 transcript variant X17	XR_007071512.1:n.	N/A	Intron Variant

Gene: MTERF4, mitochondrial transcription termination factor 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MTERF4 transcript variant 5	NM_001330179.2:c.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 6	NM_001330180.2:c.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 1	NM_182501.4:c.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 7	NR_138463.2:n.6360C>T	N/A	Non Coding Transcript Variant
MTERF4 transcript variant 2	NR_028049.2:n.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 3	NR_028050.2:n.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 4	NR_028051.2:n.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 8	NR_138464.2:n.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 9	NR_138465.2:n.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant 10	NR_138466.2:n.	N/A	Genic Downstream Transcript Variant
MTERF4 transcript variant X2	XM_047443428.1:c.160+167… XM_047443428.1:c.160+16741C>T	N/A	Intron Variant
MTERF4 transcript variant X1	XM_047443427.1:c.*3396=	N/A	3 Prime UTR Variant
MTERF4 transcript variant X3	XM_047443429.1:c.	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 2	NC_000002.12:g.241072447=	NC_000002.12:g.241072447G>A
GRCh37.p13 chr 2	NC_000002.11:g.242011862=	NC_000002.11:g.242011862G>A
MTERF4 transcript variant 7	NR_138463.2:n.6360=	NR_138463.2:n.6360C>T
MTERF4 transcript variant X1	XM_047443427.1:c.*3396=	XM_047443427.1:c.*3396C>T
SNED1 transcript	NM_001080437.1:c.3817+569=	NM_001080437.1:c.3817+569G>A
SNED1 transcript	NM_001080437.3:c.3817+569=	NM_001080437.3:c.3817+569G>A
SNED1 transcript variant X1	XM_005246997.1:c.3817+569=	XM_005246997.1:c.3817+569G>A
SNED1 transcript variant X2	XM_005246998.1:c.3817+569=	XM_005246998.1:c.3817+569G>A
SNED1 transcript variant X2	XM_011510931.3:c.3889+569=	XM_011510931.3:c.3889+569G>A
SNED1 transcript variant X7	XM_011510932.3:c.3889+569=	XM_011510932.3:c.3889+569G>A
SNED1 transcript variant X15	XM_011510934.4:c.3890-324=	XM_011510934.4:c.3890-324G>A
SNED1 transcript variant X13	XM_024452784.2:c.3889+569=	XM_024452784.2:c.3889+569G>A
MTERF4 transcript variant X2	XM_047443428.1:c.*160+16741=	XM_047443428.1:c.*160+16741C>T
SNED1 transcript variant X3	XM_047443884.1:c.3889+569=	XM_047443884.1:c.3889+569G>A
SNED1 transcript variant X8	XM_047443885.1:c.3775+569=	XM_047443885.1:c.3775+569G>A
SNED1 transcript variant X10	XM_047443886.1:c.3817+569=	XM_047443886.1:c.3817+569G>A
SNED1 transcript variant X11	XM_047443887.1:c.3703+569=	XM_047443887.1:c.3703+569G>A
SNED1 transcript variant X12	XM_047443888.1:c.3775+569=	XM_047443888.1:c.3775+569G>A
SNED1 transcript variant X14	XM_047443889.1:c.3703+569=	XM_047443889.1:c.3703+569G>A
SNED1 transcript variant X19	XM_047443890.1:c.*48+569=	XM_047443890.1:c.*48+569G>A
SNED1 transcript variant X20	XM_047443891.1:c.*48+569=	XM_047443891.1:c.*48+569G>A

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#.

53 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss6063181	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss9930146	Jul 11, 2003 (116)
3	HGSV	ss82303737	Dec 15, 2007 (130)
4	HGSV	ss82626505	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss91608749	Mar 24, 2008 (129)
6	BGI	ss103709639	Dec 01, 2009 (131)
7	ENSEMBL	ss138660763	Dec 01, 2009 (131)
8	GMI	ss154949464	Dec 01, 2009 (131)
9	BCM-HGSC-SUB	ss205925916	Jul 04, 2010 (132)
10	1000GENOMES	ss231661713	Jul 14, 2010 (132)
11	1000GENOMES	ss239104939	Jul 15, 2010 (132)
12	GMI	ss276966976	May 04, 2012 (137)
13	PJP	ss292522178	May 09, 2011 (134)
14	SSMP	ss650010776	Apr 25, 2013 (138)
15	EVA-GONL	ss978154385	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1070084531	Aug 21, 2014 (142)
17	1000GENOMES	ss1302373443	Aug 21, 2014 (142)
18	EVA_GENOME_DK	ss1579399109	Apr 01, 2015 (144)
19	EVA_DECODE	ss1587613518	Apr 01, 2015 (144)
20	WEILL_CORNELL_DGM	ss1921405136	Feb 12, 2016 (147)
21	JJLAB	ss2021251208	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2149319293	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2240646466	Dec 20, 2016 (150)
24	GRF	ss2703975248	Nov 08, 2017 (151)
25	GNOMAD	ss2788359145	Nov 08, 2017 (151)
26	SWEGEN	ss2991654621	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3024386739	Nov 08, 2017 (151)
28	CSHL	ss3344828975	Nov 08, 2017 (151)
29	EGCUT_WGS	ss3659553520	Jul 13, 2019 (153)
30	EVA_DECODE	ss3706387021	Jul 13, 2019 (153)
31	ACPOP	ss3729535478	Jul 13, 2019 (153)
32	EVA	ss3758314776	Jul 13, 2019 (153)
33	PACBIO	ss3784203429	Jul 13, 2019 (153)
34	PACBIO	ss3789735160	Jul 13, 2019 (153)
35	PACBIO	ss3794608800	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3802674598	Jul 13, 2019 (153)
37	EVA	ss3827602833	Apr 25, 2020 (154)
38	SGDP_PRJ	ss3854986825	Apr 25, 2020 (154)
39	KRGDB	ss3900746676	Apr 25, 2020 (154)
40	TOPMED	ss4550735618	Apr 26, 2021 (155)
41	TOMMO_GENOMICS	ss5157324095	Apr 26, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5252673298	Oct 13, 2022 (156)
43	EVA	ss5337211946	Oct 13, 2022 (156)
44	HUGCELL_USP	ss5452220009	Oct 13, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5530324879	Oct 13, 2022 (156)
46	SANFORD_IMAGENETICS	ss5631319275	Oct 13, 2022 (156)
47	TOMMO_GENOMICS	ss5688458394	Oct 13, 2022 (156)
48	YY_MCH	ss5803383077	Oct 13, 2022 (156)
49	EVA	ss5821846264	Oct 13, 2022 (156)
50	EVA	ss5853029988	Oct 13, 2022 (156)
51	EVA	ss5935444788	Oct 13, 2022 (156)
52	EVA	ss5957589601	Oct 13, 2022 (156)
53	EVA	ss5980124194	Oct 13, 2022 (156)
54	1000Genomes	NC_000002.11 - 242011862	Oct 11, 2018 (152)
55	1000Genomes_30x	NC_000002.12 - 241072447	Oct 13, 2022 (156)
56	Genetic variation in the Estonian population	NC_000002.11 - 242011862	Oct 11, 2018 (152)
57	The Danish reference pan genome	NC_000002.11 - 242011862	Apr 25, 2020 (154)
58	gnomAD - Genomes	NC_000002.12 - 241072447	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000002.11 - 242011862	Apr 25, 2020 (154)
60	KOREAN population from KRGDB	NC_000002.11 - 242011862	Apr 25, 2020 (154)
61	Northern Sweden	NC_000002.11 - 242011862	Jul 13, 2019 (153)
62	Qatari	NC_000002.11 - 242011862	Apr 25, 2020 (154)
63	SGDP_PRJ	NC_000002.11 - 242011862	Apr 25, 2020 (154)
64	Siberian	NC_000002.11 - 242011862	Apr 25, 2020 (154)
65	8.3KJPN	NC_000002.11 - 242011862	Apr 26, 2021 (155)
66	14KJPN	NC_000002.12 - 241072447	Oct 13, 2022 (156)
67	TopMed	NC_000002.12 - 241072447	Apr 26, 2021 (155)
68	A Vietnamese Genetic Variation Database	NC_000002.11 - 242011862	Jul 13, 2019 (153)
69	ALFA	NC_000002.12 - 241072447	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)
rs59102388	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82303737, ss82626505	NC_000002.9:241731851:G:A	NC_000002.12:241072446:G:A	(self)
ss91608749, ss205925916, ss276966976, ss292522178, ss1587613518	NC_000002.10:241660534:G:A	NC_000002.12:241072446:G:A	(self)
13504412, 5291768, 5564048, 3280743, 7924070, 2820343, 3447066, 7003805, 1835647, 15293402, 1626265, ss231661713, ss239104939, ss650010776, ss978154385, ss1070084531, ss1302373443, ss1579399109, ss1921405136, ss2021251208, ss2149319293, ss2703975248, ss2788359145, ss2991654621, ss3344828975, ss3659553520, ss3729535478, ss3758314776, ss3784203429, ss3789735160, ss3794608800, ss3827602833, ss3854986825, ss3900746676, ss5157324095, ss5337211946, ss5631319275, ss5821846264, ss5957589601, ss5980124194	NC_000002.11:242011861:G:A	NC_000002.12:241072446:G:A	(self)
17850814, 96081491, 22295498, 354558497, 318744064, ss2240646466, ss3024386739, ss3706387021, ss3802674598, ss4550735618, ss5252673298, ss5452220009, ss5530324879, ss5688458394, ss5803383077, ss5853029988, ss5935444788	NC_000002.12:241072446:G:A	NC_000002.12:241072446:G:A	(self)
ss9930146	NT_005416.10:1181841:G:A	NC_000002.12:241072446:G:A	(self)
ss6063181, ss103709639, ss138660763, ss154949464	NT_005416.13:1202729:G:A	NC_000002.12:241072446: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 rs4502400

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

rs4502400