Name: rs7304981
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.

rs7304981

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:1862352 (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: G=0.103022 (27269/264690, TOPMED)
G=0.107729 (15106/140222, GnomAD)
G=0.11343 (4526/39902, ALFA) (+ 18 more)
G=0.02389 (675/28258, 14KJPN)
G=0.02273 (381/16760, 8.3KJPN)
G=0.0868 (556/6404, 1000G_30x)
G=0.0879 (440/5008, 1000G)
G=0.1493 (669/4480, Estonian)
G=0.1059 (408/3854, ALSPAC)
G=0.1181 (438/3708, TWINSUK)
G=0.0424 (124/2922, KOREAN)
G=0.0355 (65/1832, Korea1K)
G=0.094 (94/998, GoNL)
G=0.087 (52/600, NorthernSweden)
G=0.093 (20/216, Qatari)
G=0.014 (3/214, Vietnamese)
T=0.49 (39/80, SGDP_PRJ)
G=0.08 (6/72, Ancient Sardinia)
G=0.20 (8/40, GENOME_DK)
T=0.5 (5/10, Siberian)
G=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CACNA2D4 : 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	39996	T=0.88649	G=0.11351
European	Sub	30916	T=0.88385	G=0.11615
African	Sub	5800	T=0.8884	G=0.1116
African Others	Sub	208	T=0.875	G=0.125
African American	Sub	5592	T=0.8889	G=0.1111
Asian	Sub	128	T=0.977	G=0.023
East Asian	Sub	100	T=0.98	G=0.02
Other Asian	Sub	28	T=0.96	G=0.04
Latin American 1	Sub	168	T=0.911	G=0.089
Latin American 2	Sub	700	T=0.919	G=0.081
South Asian	Sub	114	T=0.912	G=0.088
Other	Sub	2170	T=0.9000	G=0.1000

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	T=0.896978	G=0.103022
gnomAD - Genomes	Global	Study-wide	140222	T=0.892271	G=0.107729
gnomAD - Genomes	European	Sub	75928	T=0.88540	G=0.11460
gnomAD - Genomes	African	Sub	42030	T=0.88927	G=0.11073
gnomAD - Genomes	American	Sub	13660	T=0.91750	G=0.08250
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.8901	G=0.1099
gnomAD - Genomes	East Asian	Sub	3134	T=0.9761	G=0.0239
gnomAD - Genomes	Other	Sub	2150	T=0.9144	G=0.0856
Allele Frequency Aggregator	Total	Global	39902	T=0.88657	G=0.11343
Allele Frequency Aggregator	European	Sub	30840	T=0.88392	G=0.11608
Allele Frequency Aggregator	African	Sub	5800	T=0.8884	G=0.1116
Allele Frequency Aggregator	Other	Sub	2152	T=0.9006	G=0.0994
Allele Frequency Aggregator	Latin American 2	Sub	700	T=0.919	G=0.081
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.911	G=0.089
Allele Frequency Aggregator	Asian	Sub	128	T=0.977	G=0.023
Allele Frequency Aggregator	South Asian	Sub	114	T=0.912	G=0.088
14KJPN	JAPANESE	Study-wide	28258	T=0.97611	G=0.02389
8.3KJPN	JAPANESE	Study-wide	16760	T=0.97727	G=0.02273
1000Genomes_30x	Global	Study-wide	6404	T=0.9132	G=0.0868
1000Genomes_30x	African	Sub	1786	T=0.8914	G=0.1086
1000Genomes_30x	Europe	Sub	1266	T=0.8776	G=0.1224
1000Genomes_30x	South Asian	Sub	1202	T=0.9118	G=0.0882
1000Genomes_30x	East Asian	Sub	1170	T=0.9744	G=0.0256
1000Genomes_30x	American	Sub	980	T=0.928	G=0.072
1000Genomes	Global	Study-wide	5008	T=0.9121	G=0.0879
1000Genomes	African	Sub	1322	T=0.8926	G=0.1074
1000Genomes	East Asian	Sub	1008	T=0.9742	G=0.0258
1000Genomes	Europe	Sub	1006	T=0.8708	G=0.1292
1000Genomes	South Asian	Sub	978	T=0.904	G=0.096
1000Genomes	American	Sub	694	T=0.931	G=0.069
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8507	G=0.1493
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8941	G=0.1059
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8819	G=0.1181
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9576	G=0.0424
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9645	G=0.0355
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.906	G=0.094
Northern Sweden	ACPOP	Study-wide	600	T=0.913	G=0.087
Qatari	Global	Study-wide	216	T=0.907	G=0.093
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.986	G=0.014
SGDP_PRJ	Global	Study-wide	80	T=0.49	G=0.51
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	72	T=0.92	G=0.08
The Danish reference pan genome	Danish	Study-wide	40	T=0.80	G=0.20
Siberian	Global	Study-wide	10	T=0.5	G=0.5

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 12	NC_000012.12:g.1862352T>G
GRCh37.p13 chr 12	NC_000012.11:g.1971518T>G
CACNA2D4 RefSeqGene	NG_012663.2:g.61353A>C
GRCh38.p14 chr 12 fix patch HG1815_PATCH	NW_018654718.1:g.204496T>G

Gene: CACNA2D4, calcium voltage-gated channel auxiliary subunit alpha2delta 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA2D4 transcript	NM_172364.5:c.1879-2146A>C	N/A	Intron Variant
CACNA2D4 transcript variant X1	XM_011521041.3:c.1816-214… XM_011521041.3:c.1816-2146A>C	N/A	Intron Variant
CACNA2D4 transcript variant X2	XM_047429897.1:c.1807-214… XM_047429897.1:c.1807-2146A>C	N/A	Intron Variant
CACNA2D4 transcript variant X3	XM_047429898.1:c.1879-214… XM_047429898.1:c.1879-2146A>C	N/A	Intron Variant
CACNA2D4 transcript variant X4	XM_047429899.1:c.1807-214… XM_047429899.1:c.1807-2146A>C	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 12	NC_000012.12:g.1862352=	NC_000012.12:g.1862352T>G
GRCh37.p13 chr 12	NC_000012.11:g.1971518=	NC_000012.11:g.1971518T>G
CACNA2D4 RefSeqGene	NG_012663.2:g.61353=	NG_012663.2:g.61353A>C
GRCh38.p14 chr 12 fix patch HG1815_PATCH	NW_018654718.1:g.204496=	NW_018654718.1:g.204496T>G
CACNA2D4 transcript	NM_172364.4:c.1879-2146=	NM_172364.4:c.1879-2146A>C
CACNA2D4 transcript	NM_172364.5:c.1879-2146=	NM_172364.5:c.1879-2146A>C
CACNA2D4 transcript variant X1	XM_011521041.3:c.1816-2146=	XM_011521041.3:c.1816-2146A>C
CACNA2D4 transcript variant X2	XM_047429897.1:c.1807-2146=	XM_047429897.1:c.1807-2146A>C
CACNA2D4 transcript variant X3	XM_047429898.1:c.1879-2146=	XM_047429898.1:c.1879-2146A>C
CACNA2D4 transcript variant X4	XM_047429899.1:c.1807-2146=	XM_047429899.1:c.1807-2146A>C

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#.

67 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss11033820	Jul 11, 2003 (116)
2	SSAHASNP	ss35299096	May 24, 2005 (125)
3	ABI	ss40134312	Mar 14, 2006 (126)
4	1000GENOMES	ss111369020	Jan 25, 2009 (130)
5	GMI	ss157012642	Dec 01, 2009 (131)
6	BCM-HGSC-SUB	ss208083496	Jul 04, 2010 (132)
7	1000GENOMES	ss225568042	Jul 14, 2010 (132)
8	1000GENOMES	ss235795587	Jul 15, 2010 (132)
9	1000GENOMES	ss242379591	Jul 15, 2010 (132)
10	GMI	ss281244274	May 04, 2012 (137)
11	PJP	ss291237879	May 09, 2011 (134)
12	ILLUMINA	ss483035739	May 04, 2012 (137)
13	ILLUMINA	ss484355835	May 04, 2012 (137)
14	ILLUMINA	ss536538388	Sep 08, 2015 (146)
15	TISHKOFF	ss562949318	Apr 25, 2013 (138)
16	SSMP	ss658474565	Apr 25, 2013 (138)
17	ILLUMINA	ss780622647	Aug 21, 2014 (142)
18	ILLUMINA	ss782624135	Aug 21, 2014 (142)
19	ILLUMINA	ss836116290	Aug 21, 2014 (142)
20	EVA-GONL	ss989164703	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1078195350	Aug 21, 2014 (142)
22	1000GENOMES	ss1343727165	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1576070425	Apr 01, 2015 (144)
24	EVA_DECODE	ss1598835937	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1627875415	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1670869448	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1807085844	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1932525047	Feb 12, 2016 (147)
29	JJLAB	ss2027009662	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2155328154	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2187259317	Dec 20, 2016 (150)
32	ILLUMINA	ss2632914791	Nov 08, 2017 (151)
33	GRF	ss2699647068	Nov 08, 2017 (151)
34	GNOMAD	ss2906569554	Nov 08, 2017 (151)
35	AFFY	ss2984964584	Nov 08, 2017 (151)
36	AFFY	ss2985608331	Nov 08, 2017 (151)
37	SWEGEN	ss3009087710	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3027307562	Nov 08, 2017 (151)
39	CSHL	ss3349886685	Nov 08, 2017 (151)
40	ILLUMINA	ss3626797763	Oct 12, 2018 (152)
41	ILLUMINA	ss3630927060	Oct 12, 2018 (152)
42	ILLUMINA	ss3641770701	Oct 12, 2018 (152)
43	URBANLAB	ss3649746997	Oct 12, 2018 (152)
44	ILLUMINA	ss3653736812	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3676418651	Jul 13, 2019 (153)
46	EVA_DECODE	ss3692974765	Jul 13, 2019 (153)
47	ACPOP	ss3738707860	Jul 13, 2019 (153)
48	EVA	ss3750053532	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3815371420	Jul 13, 2019 (153)
50	EVA	ss3832936970	Apr 26, 2020 (154)
51	SGDP_PRJ	ss3877537908	Apr 26, 2020 (154)
52	KRGDB	ss3926031962	Apr 26, 2020 (154)
53	KOGIC	ss3971135235	Apr 26, 2020 (154)
54	EVA	ss3985570584	Apr 26, 2021 (155)
55	TOPMED	ss4906404631	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5204745459	Apr 26, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5289562650	Oct 18, 2022 (156)
58	EVA	ss5315593954	Oct 18, 2022 (156)
59	EVA	ss5403478906	Oct 18, 2022 (156)
60	HUGCELL_USP	ss5484482443	Oct 18, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5586371635	Oct 18, 2022 (156)
62	SANFORD_IMAGENETICS	ss5652449665	Oct 18, 2022 (156)
63	TOMMO_GENOMICS	ss5753442908	Oct 18, 2022 (156)
64	YY_MCH	ss5812942463	Oct 18, 2022 (156)
65	EVA	ss5837491040	Oct 18, 2022 (156)
66	EVA	ss5903014317	Oct 18, 2022 (156)
67	EVA	ss5943797612	Oct 18, 2022 (156)
68	1000Genomes	NC_000012.11 - 1971518	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000012.12 - 1862352	Oct 18, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 1971518	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000012.11 - 1971518	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000012.11 - 1971518	Apr 26, 2020 (154)
73	gnomAD - Genomes	NC_000012.12 - 1862352	Apr 26, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000012.11 - 1971518	Apr 26, 2020 (154)
75	KOREAN population from KRGDB	NC_000012.11 - 1971518	Apr 26, 2020 (154)
76	Korean Genome Project	NC_000012.12 - 1862352	Apr 26, 2020 (154)
77	Northern Sweden	NC_000012.11 - 1971518	Jul 13, 2019 (153)
78	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000012.11 - 1971518	Apr 26, 2021 (155)
79	Qatari	NC_000012.11 - 1971518	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000012.11 - 1971518	Apr 26, 2020 (154)
81	Siberian	NC_000012.11 - 1971518	Apr 26, 2020 (154)
82	8.3KJPN	NC_000012.11 - 1971518	Apr 26, 2021 (155)
83	14KJPN	NC_000012.12 - 1862352	Oct 18, 2022 (156)
84	TopMed	NC_000012.12 - 1862352	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000012.11 - 1971518	Oct 12, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000012.11 - 1971518	Jul 13, 2019 (153)
87	ALFA	NC_000012.12 - 1862352	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35299096	NC_000012.9:1841778:T:G	NC_000012.12:1862351:T:G	(self)
ss111369020, ss208083496, ss281244274, ss291237879, ss483035739, ss1598835937	NC_000012.10:1841778:T:G	NC_000012.12:1862351:T:G	(self)
56335983, 31284728, 22156899, 2813969, 13956488, 33209356, 11992725, 796511, 14566977, 29554888, 7844508, 62714766, 31284728, 6940435, ss225568042, ss235795587, ss242379591, ss484355835, ss536538388, ss562949318, ss658474565, ss780622647, ss782624135, ss836116290, ss989164703, ss1078195350, ss1343727165, ss1576070425, ss1627875415, ss1670869448, ss1807085844, ss1932525047, ss2027009662, ss2155328154, ss2632914791, ss2699647068, ss2906569554, ss2984964584, ss2985608331, ss3009087710, ss3349886685, ss3626797763, ss3630927060, ss3641770701, ss3653736812, ss3676418651, ss3738707860, ss3750053532, ss3832936970, ss3877537908, ss3926031962, ss3985570584, ss5204745459, ss5315593954, ss5403478906, ss5652449665, ss5837491040, ss5943797612	NC_000012.11:1971517:T:G	NC_000012.12:1862351:T:G	(self)
73897570, 397330391, 27513236, 87280012, 121950288, 5345217161, ss2187259317, ss3027307562, ss3649746997, ss3692974765, ss3815371420, ss3971135235, ss4906404631, ss5289562650, ss5484482443, ss5586371635, ss5753442908, ss5812942463, ss5903014317	NC_000012.12:1862351:T:G	NC_000012.12:1862351:T:G	(self)
ss11033820	NT_009759.15:1825778:T:G	NC_000012.12:1862351:T:G	(self)
ss40134312, ss157012642	NT_009759.16:1911517:T:G	NC_000012.12:1862351: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 rs7304981

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs7304981