Name: rs4652662
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.

rs4652662

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:181536862 (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: T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.007643 (2023/264690, TOPMED)
T=0.007561 (1058/139932, GnomAD)
T=0.00000 (0/28256, 14KJPN) (+ 14 more)
T=0.00405 (75/18520, ALFA)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0059 (38/6404, 1000G_30x)
T=0.0056 (28/5008, 1000G)
T=0.0000 (0/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.0000 (0/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.000 (0/600, NorthernSweden)
T=0.002 (1/558, SGDP_PRJ)
T=0.005 (1/216, Qatari)
T=0.000 (0/212, Vietnamese)
T=0.00 (0/56, Siberian)
T=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CACNA1E : 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	18520	T=0.00405	G=0.99595
European	Sub	14152	T=0.00007	G=0.99993
African	Sub	2898	T=0.0245	G=0.9755
African Others	Sub	114	T=0.044	G=0.956
African American	Sub	2784	T=0.0237	G=0.9763
Asian	Sub	112	T=0.000	G=1.000
East Asian	Sub	86	T=0.00	G=1.00
Other Asian	Sub	26	T=0.00	G=1.00
Latin American 1	Sub	146	T=0.007	G=0.993
Latin American 2	Sub	610	T=0.000	G=1.000
South Asian	Sub	98	T=0.00	G=1.00
Other	Sub	504	T=0.004	G=0.996

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	T=0.007643	G=0.992357
gnomAD - Genomes	Global	Study-wide	139932	T=0.007561	G=0.992439
gnomAD - Genomes	European	Sub	75866	T=0.00012	G=0.99988
gnomAD - Genomes	African	Sub	41852	T=0.02401	G=0.97599
gnomAD - Genomes	American	Sub	13618	T=0.00228	G=0.99772
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.0000	G=1.0000
gnomAD - Genomes	East Asian	Sub	3130	T=0.0000	G=1.0000
gnomAD - Genomes	Other	Sub	2144	T=0.0061	G=0.9939
14KJPN	JAPANESE	Study-wide	28256	T=0.00000	G=1.00000
Allele Frequency Aggregator	Total	Global	18520	T=0.00405	G=0.99595
Allele Frequency Aggregator	European	Sub	14152	T=0.00007	G=0.99993
Allele Frequency Aggregator	African	Sub	2898	T=0.0245	G=0.9755
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.000	G=1.000
Allele Frequency Aggregator	Other	Sub	504	T=0.004	G=0.996
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.007	G=0.993
Allele Frequency Aggregator	Asian	Sub	112	T=0.000	G=1.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.00	G=1.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00000	G=1.00000
1000Genomes_30x	Global	Study-wide	6404	T=0.0059	G=0.9941
1000Genomes_30x	African	Sub	1786	T=0.0213	G=0.9787
1000Genomes_30x	Europe	Sub	1266	T=0.0000	G=1.0000
1000Genomes_30x	South Asian	Sub	1202	T=0.0000	G=1.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.0000	G=1.0000
1000Genomes_30x	American	Sub	980	T=0.000	G=1.000
1000Genomes	Global	Study-wide	5008	T=0.0056	G=0.9944
1000Genomes	African	Sub	1322	T=0.0212	G=0.9788
1000Genomes	East Asian	Sub	1008	T=0.0000	G=1.0000
1000Genomes	Europe	Sub	1006	T=0.0000	G=1.0000
1000Genomes	South Asian	Sub	978	T=0.000	G=1.000
1000Genomes	American	Sub	694	T=0.000	G=1.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0000	G=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0000	G=1.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0000	G=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	G=1.0000
Northern Sweden	ACPOP	Study-wide	600	T=0.000	G=1.000
SGDP_PRJ	Global	Study-wide	558	T=0.002	G=0.998
Qatari	Global	Study-wide	216	T=0.005	G=0.995
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.000	G=1.000
Siberian	Global	Study-wide	56	T=0.00	G=1.00
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	G=1.00

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.181536862T>G
GRCh37.p13 chr 1	NC_000001.10:g.181505998T>G
CACNA1E RefSeqGene	NG_050616.1:g.58552T>G

Gene: CACNA1E, calcium voltage-gated channel subunit alpha1 E (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA1E transcript variant 3	NM_000721.4:c.512+25352T>G	N/A	Intron Variant
CACNA1E transcript variant 1	NM_001205293.3:c.512+2535… NM_001205293.3:c.512+25352T>G	N/A	Intron Variant
CACNA1E transcript variant 2	NM_001205294.2:c.512+2535… NM_001205294.2:c.512+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X1	XM_017002243.2:c.947+2535… XM_017002243.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X2	XM_017002244.2:c.947+2535… XM_017002244.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X3	XM_017002245.2:c.947+2535… XM_017002245.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X4	XM_017002246.2:c.947+2535… XM_017002246.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X5	XM_017002247.2:c.947+2535… XM_017002247.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X6	XM_017002248.2:c.947+2535… XM_017002248.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X8	XM_017002249.2:c.947+2535… XM_017002249.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X9	XM_017002250.2:c.947+2535… XM_017002250.2:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X10	XM_017002251.1:c.947+2535… XM_017002251.1:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X7	XM_047429979.1:c.947+2535… XM_047429979.1:c.947+25352T>G	N/A	Intron Variant
CACNA1E transcript variant X11	XM_047429980.1:c.947+2535… XM_047429980.1:c.947+25352T>G	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	T=	G
GRCh38.p14 chr 1	NC_000001.11:g.181536862=	NC_000001.11:g.181536862T>G
GRCh37.p13 chr 1	NC_000001.10:g.181505998=	NC_000001.10:g.181505998T>G
CACNA1E RefSeqGene	NG_050616.1:g.58552=	NG_050616.1:g.58552T>G
CACNA1E transcript variant 3	NM_000721.3:c.512+25352=	NM_000721.3:c.512+25352T>G
CACNA1E transcript variant 3	NM_000721.4:c.512+25352=	NM_000721.4:c.512+25352T>G
CACNA1E transcript variant 1	NM_001205293.1:c.512+25352=	NM_001205293.1:c.512+25352T>G
CACNA1E transcript variant 1	NM_001205293.3:c.512+25352=	NM_001205293.3:c.512+25352T>G
CACNA1E transcript variant 2	NM_001205294.1:c.512+25352=	NM_001205294.1:c.512+25352T>G
CACNA1E transcript variant 2	NM_001205294.2:c.512+25352=	NM_001205294.2:c.512+25352T>G
CACNA1E transcript variant X1	XM_005245477.1:c.512+25352=	XM_005245477.1:c.512+25352T>G
CACNA1E transcript variant X1	XM_017002243.2:c.947+25352=	XM_017002243.2:c.947+25352T>G
CACNA1E transcript variant X2	XM_017002244.2:c.947+25352=	XM_017002244.2:c.947+25352T>G
CACNA1E transcript variant X3	XM_017002245.2:c.947+25352=	XM_017002245.2:c.947+25352T>G
CACNA1E transcript variant X4	XM_017002246.2:c.947+25352=	XM_017002246.2:c.947+25352T>G
CACNA1E transcript variant X5	XM_017002247.2:c.947+25352=	XM_017002247.2:c.947+25352T>G
CACNA1E transcript variant X6	XM_017002248.2:c.947+25352=	XM_017002248.2:c.947+25352T>G
CACNA1E transcript variant X8	XM_017002249.2:c.947+25352=	XM_017002249.2:c.947+25352T>G
CACNA1E transcript variant X9	XM_017002250.2:c.947+25352=	XM_017002250.2:c.947+25352T>G
CACNA1E transcript variant X10	XM_017002251.1:c.947+25352=	XM_017002251.1:c.947+25352T>G
CACNA1E transcript variant X7	XM_047429979.1:c.947+25352=	XM_047429979.1:c.947+25352T>G
CACNA1E transcript variant X11	XM_047429980.1:c.947+25352=	XM_047429980.1:c.947+25352T>G

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#.

77 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6403078	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss9842362	Jul 11, 2003 (116)
3	WI_SSAHASNP	ss11373013	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss19149276	Feb 27, 2004 (120)
5	SSAHASNP	ss20546217	Apr 05, 2004 (121)
6	HGSV	ss77200611	Dec 07, 2007 (129)
7	HGSV	ss82020344	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss87889319	Mar 23, 2008 (129)
9	HUMANGENOME_JCVI	ss97987547	Feb 04, 2009 (130)
10	BGI	ss106614840	Feb 04, 2009 (130)
11	1000GENOMES	ss108749726	Jan 23, 2009 (130)
12	1000GENOMES	ss111434405	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss119117840	Feb 15, 2009 (130)
14	ENSEMBL	ss138114281	Dec 01, 2009 (131)
15	ENSEMBL	ss142556470	Dec 01, 2009 (131)
16	GMI	ss155993190	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss164575108	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss165513881	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss167337960	Jul 04, 2010 (132)
20	BUSHMAN	ss199320063	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss205212257	Jul 04, 2010 (132)
22	1000GENOMES	ss218751047	Jul 14, 2010 (132)
23	1000GENOMES	ss230805657	Jul 14, 2010 (132)
24	BL	ss253649634	May 09, 2011 (134)
25	GMI	ss276123395	May 04, 2012 (137)
26	GMI	ss284185484	Apr 25, 2013 (138)
27	PJP	ss290675544	May 09, 2011 (134)
28	TISHKOFF	ss554916097	Apr 25, 2013 (138)
29	SSMP	ss648538068	Apr 25, 2013 (138)
30	JMKIDD_LAB	ss1068412263	Aug 21, 2014 (142)
31	1000GENOMES	ss1293671744	Aug 21, 2014 (142)
32	DDI	ss1426036318	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1574517118	Apr 01, 2015 (144)
34	EVA_DECODE	ss1585268714	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1601613182	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1644607215	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1795362325	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1919115057	Feb 12, 2016 (147)
39	GENOMED	ss1966912332	Jul 19, 2016 (147)
40	JJLAB	ss2020073631	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2148101331	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2168065611	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2624545244	Nov 08, 2017 (151)
44	GRF	ss2698083097	Nov 08, 2017 (151)
45	GNOMAD	ss2763430157	Nov 08, 2017 (151)
46	SWEGEN	ss2988052495	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3023796534	Nov 08, 2017 (151)
48	CSHL	ss3343798521	Nov 08, 2017 (151)
49	URBANLAB	ss3646832173	Oct 11, 2018 (152)
50	EVA_DECODE	ss3688145577	Jul 12, 2019 (153)
51	ACPOP	ss3727647864	Jul 12, 2019 (153)
52	EVA	ss3747035984	Jul 12, 2019 (153)
53	PACBIO	ss3783620972	Jul 12, 2019 (153)
54	PACBIO	ss3789243689	Jul 12, 2019 (153)
55	PACBIO	ss3794115821	Jul 12, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3800036974	Jul 12, 2019 (153)
57	EVA	ss3826521336	Apr 25, 2020 (154)
58	EVA	ss3836657211	Apr 25, 2020 (154)
59	EVA	ss3842067468	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3850389614	Apr 25, 2020 (154)
61	KRGDB	ss3895648025	Apr 25, 2020 (154)
62	KOGIC	ss3946019727	Apr 25, 2020 (154)
63	TOPMED	ss4474883040	Apr 25, 2021 (155)
64	TOMMO_GENOMICS	ss5147324310	Apr 25, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5244938867	Oct 12, 2022 (156)
66	EVA	ss5323232058	Oct 12, 2022 (156)
67	HUGCELL_USP	ss5445459313	Oct 12, 2022 (156)
68	EVA	ss5506098168	Oct 12, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5518593035	Oct 12, 2022 (156)
70	SANFORD_IMAGENETICS	ss5626959965	Oct 12, 2022 (156)
71	TOMMO_GENOMICS	ss5674766282	Oct 12, 2022 (156)
72	YY_MCH	ss5801421284	Oct 12, 2022 (156)
73	EVA	ss5832921691	Oct 12, 2022 (156)
74	EVA	ss5849182415	Oct 12, 2022 (156)
75	EVA	ss5910989523	Oct 12, 2022 (156)
76	EVA	ss5938773156	Oct 12, 2022 (156)
77	EVA	ss5980001963	Oct 12, 2022 (156)
78	1000Genomes	NC_000001.10 - 181505998	Oct 11, 2018 (152)
79	1000Genomes_30x	NC_000001.11 - 181536862	Oct 12, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 181505998	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000001.10 - 181505998	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000001.11 - 181536862	Apr 25, 2021 (155)
83	KOREAN population from KRGDB	NC_000001.10 - 181505998	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000001.11 - 181536862	Apr 25, 2020 (154)
85	Northern Sweden	NC_000001.10 - 181505998	Jul 12, 2019 (153)
86	Qatari	NC_000001.10 - 181505998	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000001.10 - 181505998	Apr 25, 2020 (154)
88	Siberian	NC_000001.10 - 181505998	Apr 25, 2020 (154)
89	8.3KJPN	NC_000001.10 - 181505998	Apr 25, 2021 (155)
90	14KJPN	NC_000001.11 - 181536862	Oct 12, 2022 (156)
91	TopMed	NC_000001.11 - 181536862	Apr 25, 2021 (155)
92	UK 10K study - Twins	NC_000001.10 - 181505998	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000001.10 - 181505998	Jul 12, 2019 (153)
94	ALFA	NC_000001.11 - 181536862	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).

Associated ID	History Updated (Build)
rs58351425	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77200611, ss82020344	NC_000001.8:178237654:T:G	NC_000001.11:181536861:T:G	(self)
ss87889319, ss108749726, ss111434405, ss119117840, ss164575108, ss165513881, ss167337960, ss199320063, ss205212257, ss253649634, ss276123395, ss284185484, ss290675544, ss1585268714	NC_000001.9:179772620:T:G	NC_000001.11:181536861:T:G	(self)
4489924, 2459383, 1784950, 2825419, 932729, 1156987, 2406594, 617685, 5293617, 2459383, 527404, ss218751047, ss230805657, ss554916097, ss648538068, ss1068412263, ss1293671744, ss1426036318, ss1574517118, ss1601613182, ss1644607215, ss1795362325, ss1919115057, ss1966912332, ss2020073631, ss2148101331, ss2624545244, ss2698083097, ss2763430157, ss2988052495, ss3343798521, ss3727647864, ss3747035984, ss3783620972, ss3789243689, ss3794115821, ss3826521336, ss3836657211, ss3850389614, ss3895648025, ss5147324310, ss5323232058, ss5506098168, ss5626959965, ss5832921691, ss5938773156, ss5980001963	NC_000001.10:181505997:T:G	NC_000001.11:181536861:T:G	(self)
6118970, 32429525, 2397728, 8603386, 38489375, 5607870869, ss2168065611, ss3023796534, ss3646832173, ss3688145577, ss3800036974, ss3842067468, ss3946019727, ss4474883040, ss5244938867, ss5445459313, ss5518593035, ss5674766282, ss5801421284, ss5849182415, ss5910989523	NC_000001.11:181536861:T:G	NC_000001.11:181536861:T:G	(self)
ss9842362, ss11373013	NT_004487.15:10299034:T:G	NC_000001.11:181536861:T:G	(self)
ss19149276, ss20546217	NT_004487.16:10554494:T:G	NC_000001.11:181536861:T:G	(self)
ss6403078, ss97987547, ss106614840, ss138114281, ss142556470, ss155993190	NT_004487.19:32994639:T:G	NC_000001.11:181536861:T:G	(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 rs4652662

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

rs4652662