Name: rs57854489
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.

rs57854489

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:1855344 (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=0.076059 (20132/264690, TOPMED)
A=0.061155 (8570/140136, GnomAD)
A=0.49625 (14023/28258, 14KJPN) (+ 17 more)
A=0.04029 (761/18890, ALFA)
A=0.49045 (8220/16760, 8.3KJPN)
A=0.1680 (1076/6404, 1000G_30x)
A=0.1741 (872/5008, 1000G)
A=0.0201 (90/4480, Estonian)
A=0.0114 (44/3854, ALSPAC)
A=0.0138 (51/3708, TWINSUK)
A=0.4283 (1255/2930, KOREAN)
A=0.4340 (795/1832, Korea1K)
A=0.008 (8/998, GoNL)
A=0.038 (23/600, NorthernSweden)
A=0.056 (12/216, Qatari)
A=0.415 (88/212, Vietnamese)
G=0.394 (71/180, SGDP_PRJ)
A=0.05 (2/40, GENOME_DK)
G=0.50 (9/18, Siberian)
A=0.50 (9/18, 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	18890	G=0.95971	A=0.04029
European	Sub	14286	G=0.98285	A=0.01715
African	Sub	2946	G=0.9036	A=0.0964
African Others	Sub	114	G=0.912	A=0.088
African American	Sub	2832	G=0.9032	A=0.0968
Asian	Sub	112	G=0.527	A=0.473
East Asian	Sub	86	G=0.52	A=0.48
Other Asian	Sub	26	G=0.54	A=0.46
Latin American 1	Sub	146	G=0.938	A=0.062
Latin American 2	Sub	610	G=0.843	A=0.157
South Asian	Sub	98	G=0.87	A=0.13
Other	Sub	692	G=0.912	A=0.088

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=0.923941	A=0.076059
gnomAD - Genomes	Global	Study-wide	140136	G=0.938845	A=0.061155
gnomAD - Genomes	European	Sub	75912	G=0.98071	A=0.01929
gnomAD - Genomes	African	Sub	41972	G=0.90434	A=0.09566
gnomAD - Genomes	American	Sub	13652	G=0.88419	A=0.11581
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9567	A=0.0433
gnomAD - Genomes	East Asian	Sub	3130	G=0.6134	A=0.3866
gnomAD - Genomes	Other	Sub	2148	G=0.9274	A=0.0726
14KJPN	JAPANESE	Study-wide	28258	G=0.50375	A=0.49625
Allele Frequency Aggregator	Total	Global	18890	G=0.95971	A=0.04029
Allele Frequency Aggregator	European	Sub	14286	G=0.98285	A=0.01715
Allele Frequency Aggregator	African	Sub	2946	G=0.9036	A=0.0964
Allele Frequency Aggregator	Other	Sub	692	G=0.912	A=0.088
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.843	A=0.157
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.938	A=0.062
Allele Frequency Aggregator	Asian	Sub	112	G=0.527	A=0.473
Allele Frequency Aggregator	South Asian	Sub	98	G=0.87	A=0.13
8.3KJPN	JAPANESE	Study-wide	16760	G=0.50955	A=0.49045
1000Genomes_30x	Global	Study-wide	6404	G=0.8320	A=0.1680
1000Genomes_30x	African	Sub	1786	G=0.9026	A=0.0974
1000Genomes_30x	Europe	Sub	1266	G=0.9834	A=0.0166
1000Genomes_30x	South Asian	Sub	1202	G=0.7862	A=0.2138
1000Genomes_30x	East Asian	Sub	1170	G=0.5829	A=0.4171
1000Genomes_30x	American	Sub	980	G=0.861	A=0.139
1000Genomes	Global	Study-wide	5008	G=0.8259	A=0.1741
1000Genomes	African	Sub	1322	G=0.9039	A=0.0961
1000Genomes	East Asian	Sub	1008	G=0.5784	A=0.4216
1000Genomes	Europe	Sub	1006	G=0.9861	A=0.0139
1000Genomes	South Asian	Sub	978	G=0.789	A=0.211
1000Genomes	American	Sub	694	G=0.856	A=0.144
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9799	A=0.0201
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9886	A=0.0114
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9862	A=0.0138
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.5717	A=0.4283
Korean Genome Project	KOREAN	Study-wide	1832	G=0.5660	A=0.4340
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.992	A=0.008
Northern Sweden	ACPOP	Study-wide	600	G=0.962	A=0.038
Qatari	Global	Study-wide	216	G=0.944	A=0.056
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.585	A=0.415
SGDP_PRJ	Global	Study-wide	180	G=0.394	A=0.606
The Danish reference pan genome	Danish	Study-wide	40	G=0.95	A=0.05
Siberian	Global	Study-wide	18	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 12	NC_000012.12:g.1855344G>A
GRCh37.p13 chr 12	NC_000012.11:g.1964510G>A
CACNA2D4 RefSeqGene	NG_012663.2:g.68361C>T
GRCh38.p14 chr 12 fix patch HG1815_PATCH	NW_018654718.1:g.197488G>A

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.2152+668C>T	N/A	Intron Variant
CACNA2D4 transcript variant X1	XM_011521041.3:c.2089+668… XM_011521041.3:c.2089+668C>T	N/A	Intron Variant
CACNA2D4 transcript variant X2	XM_047429897.1:c.2080+668… XM_047429897.1:c.2080+668C>T	N/A	Intron Variant
CACNA2D4 transcript variant X3	XM_047429898.1:c.2152+668… XM_047429898.1:c.2152+668C>T	N/A	Intron Variant
CACNA2D4 transcript variant X4	XM_047429899.1:c.2080+668… XM_047429899.1:c.2080+668C>T	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	G=	A
GRCh38.p14 chr 12	NC_000012.12:g.1855344=	NC_000012.12:g.1855344G>A
GRCh37.p13 chr 12	NC_000012.11:g.1964510=	NC_000012.11:g.1964510G>A
CACNA2D4 RefSeqGene	NG_012663.2:g.68361=	NG_012663.2:g.68361C>T
GRCh38.p14 chr 12 fix patch HG1815_PATCH	NW_018654718.1:g.197488=	NW_018654718.1:g.197488G>A
CACNA2D4 transcript	NM_172364.4:c.2152+668=	NM_172364.4:c.2152+668C>T
CACNA2D4 transcript	NM_172364.5:c.2152+668=	NM_172364.5:c.2152+668C>T
CACNA2D4 transcript variant X1	XM_011521041.3:c.2089+668=	XM_011521041.3:c.2089+668C>T
CACNA2D4 transcript variant X2	XM_047429897.1:c.2080+668=	XM_047429897.1:c.2080+668C>T
CACNA2D4 transcript variant X3	XM_047429898.1:c.2152+668=	XM_047429898.1:c.2152+668C>T
CACNA2D4 transcript variant X4	XM_047429899.1:c.2080+668=	XM_047429899.1:c.2080+668C>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#.

50 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss81525888	Dec 14, 2007 (129)
2	HGSV	ss81965623	Dec 14, 2007 (129)
3	BGI	ss103017890	Dec 01, 2009 (131)
4	ILLUMINA-UK	ss118513454	Feb 14, 2009 (130)
5	BUSHMAN	ss203454837	Jul 04, 2010 (132)
6	1000GENOMES	ss225567995	Jul 14, 2010 (132)
7	1000GENOMES	ss242379557	Jul 15, 2010 (132)
8	GMI	ss281244234	May 04, 2012 (137)
9	PJP	ss291237861	May 09, 2011 (134)
10	TISHKOFF	ss562949259	Apr 25, 2013 (138)
11	SSMP	ss658474520	Apr 25, 2013 (138)
12	EVA-GONL	ss989164629	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1078195286	Aug 21, 2014 (142)
14	1000GENOMES	ss1343726911	Aug 21, 2014 (142)
15	EVA_GENOME_DK	ss1576070369	Apr 01, 2015 (144)
16	EVA_DECODE	ss1598835858	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1627875252	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1670869285	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1932524978	Feb 12, 2016 (147)
20	GENOMED	ss1967505900	Jul 19, 2016 (147)
21	JJLAB	ss2027009617	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2155328112	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2187258854	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2627981329	Nov 08, 2017 (151)
25	GRF	ss2699647027	Nov 08, 2017 (151)
26	GNOMAD	ss2906568972	Nov 08, 2017 (151)
27	SWEGEN	ss3009087612	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3676418546	Jul 13, 2019 (153)
29	EVA_DECODE	ss3692974644	Jul 13, 2019 (153)
30	ACPOP	ss3738707806	Jul 13, 2019 (153)
31	EVA	ss3750053433	Jul 13, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3815371340	Jul 13, 2019 (153)
33	EVA	ss3832936931	Apr 26, 2020 (154)
34	SGDP_PRJ	ss3877537791	Apr 26, 2020 (154)
35	KRGDB	ss3926031850	Apr 26, 2020 (154)
36	KOGIC	ss3971135110	Apr 26, 2020 (154)
37	TOPMED	ss4906402830	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5204745245	Apr 26, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5289562459	Oct 18, 2022 (156)
40	EVA	ss5403478539	Oct 18, 2022 (156)
41	HUGCELL_USP	ss5484482254	Oct 18, 2022 (156)
42	EVA	ss5510579124	Oct 18, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5586371344	Oct 18, 2022 (156)
44	SANFORD_IMAGENETICS	ss5652449539	Oct 18, 2022 (156)
45	TOMMO_GENOMICS	ss5753442641	Oct 18, 2022 (156)
46	YY_MCH	ss5812942400	Oct 18, 2022 (156)
47	EVA	ss5837490956	Oct 18, 2022 (156)
48	EVA	ss5850230886	Oct 18, 2022 (156)
49	EVA	ss5903014070	Oct 18, 2022 (156)
50	EVA	ss5943797474	Oct 18, 2022 (156)
51	1000Genomes	NC_000012.11 - 1964510	Oct 12, 2018 (152)
52	1000Genomes_30x	NC_000012.12 - 1855344	Oct 18, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 1964510	Oct 12, 2018 (152)
54	Genetic variation in the Estonian population	NC_000012.11 - 1964510	Oct 12, 2018 (152)
55	The Danish reference pan genome	NC_000012.11 - 1964510	Apr 26, 2020 (154)
56	gnomAD - Genomes	NC_000012.12 - 1855344	Apr 26, 2021 (155)
57	Genome of the Netherlands Release 5	NC_000012.11 - 1964510	Apr 26, 2020 (154)
58	KOREAN population from KRGDB	NC_000012.11 - 1964510	Apr 26, 2020 (154)
59	Korean Genome Project	NC_000012.12 - 1855344	Apr 26, 2020 (154)
60	Northern Sweden	NC_000012.11 - 1964510	Jul 13, 2019 (153)
61	Qatari	NC_000012.11 - 1964510	Apr 26, 2020 (154)
62	SGDP_PRJ	NC_000012.11 - 1964510	Apr 26, 2020 (154)
63	Siberian	NC_000012.11 - 1964510	Apr 26, 2020 (154)
64	8.3KJPN	NC_000012.11 - 1964510	Apr 26, 2021 (155)
65	14KJPN	NC_000012.12 - 1855344	Oct 18, 2022 (156)
66	TopMed	NC_000012.12 - 1855344	Apr 26, 2021 (155)
67	UK 10K study - Twins	NC_000012.11 - 1964510	Oct 12, 2018 (152)
68	A Vietnamese Genetic Variation Database	NC_000012.11 - 1964510	Jul 13, 2019 (153)
69	ALFA	NC_000012.12 - 1855344	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
ss81525888, ss81965623	NC_000012.9:1834770:G:A	NC_000012.12:1855343:G:A	(self)
ss118513454, ss203454837, ss281244234, ss291237861, ss1598835858	NC_000012.10:1834770:G:A	NC_000012.12:1855343:G:A	(self)
56335724, 31284560, 22156794, 2813930, 13956414, 33209244, 11992671, 14566908, 29554771, 7844466, 62714552, 31284560, 6940391, ss225567995, ss242379557, ss562949259, ss658474520, ss989164629, ss1078195286, ss1343726911, ss1576070369, ss1627875252, ss1670869285, ss1932524978, ss1967505900, ss2027009617, ss2155328112, ss2627981329, ss2699647027, ss2906568972, ss3009087612, ss3676418546, ss3738707806, ss3750053433, ss3832936931, ss3877537791, ss3926031850, ss5204745245, ss5403478539, ss5510579124, ss5652449539, ss5837490956, ss5943797474	NC_000012.11:1964509:G:A	NC_000012.12:1855343:G:A	(self)
73897279, 397329008, 27513111, 87279745, 121948487, 8786279277, ss2187258854, ss3692974644, ss3815371340, ss3971135110, ss4906402830, ss5289562459, ss5484482254, ss5586371344, ss5753442641, ss5812942400, ss5850230886, ss5903014070	NC_000012.12:1855343:G:A	NC_000012.12:1855343:G:A	(self)
ss103017890	NT_009759.16:1904509:G:A	NC_000012.12:1855343: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 rs57854489

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

rs57854489