Name: rs131825
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.

rs131825

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:36650714 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.222007 (58763/264690, TOPMED)
G=0.223229 (31261/140040, GnomAD)
G=0.15911 (4496/28258, 14KJPN) (+ 16 more)
G=0.24595 (4646/18890, ALFA)
G=0.15563 (2608/16758, 8.3KJPN)
G=0.2038 (1305/6404, 1000G_30x)
G=0.2037 (1020/5008, 1000G)
G=0.2462 (1103/4480, Estonian)
G=0.2769 (1067/3854, ALSPAC)
G=0.2743 (1017/3708, TWINSUK)
G=0.1611 (472/2930, KOREAN)
G=0.296 (295/998, GoNL)
G=0.218 (131/600, NorthernSweden)
G=0.182 (95/522, SGDP_PRJ)
G=0.095 (29/304, HapMap)
G=0.245 (53/216, Qatari)
G=0.099 (21/212, Vietnamese)
G=0.11 (6/54, Siberian)
G=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CACNG2 : 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=0.24595	C=0.75405
European	Sub	14286	G=0.26942	C=0.73058
African	Sub	2946	G=0.1385	C=0.8615
African Others	Sub	114	G=0.140	C=0.860
African American	Sub	2832	G=0.1384	C=0.8616
Asian	Sub	112	G=0.188	C=0.812
East Asian	Sub	86	G=0.19	C=0.81
Other Asian	Sub	26	G=0.19	C=0.81
Latin American 1	Sub	146	G=0.301	C=0.699
Latin American 2	Sub	610	G=0.202	C=0.798
South Asian	Sub	98	G=0.31	C=0.69
Other	Sub	692	G=0.247	C=0.753

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=0.222007	C=0.777993
gnomAD - Genomes	Global	Study-wide	140040	G=0.223229	C=0.776771
gnomAD - Genomes	European	Sub	75854	G=0.26685	C=0.73315
gnomAD - Genomes	African	Sub	41960	G=0.13739	C=0.86261
gnomAD - Genomes	American	Sub	13632	G=0.22264	C=0.77736
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.3731	C=0.6269
gnomAD - Genomes	East Asian	Sub	3126	G=0.1456	C=0.8544
gnomAD - Genomes	Other	Sub	2150	G=0.2447	C=0.7553
14KJPN	JAPANESE	Study-wide	28258	G=0.15911	C=0.84089
Allele Frequency Aggregator	Total	Global	18890	G=0.24595	C=0.75405
Allele Frequency Aggregator	European	Sub	14286	G=0.26942	C=0.73058
Allele Frequency Aggregator	African	Sub	2946	G=0.1385	C=0.8615
Allele Frequency Aggregator	Other	Sub	692	G=0.247	C=0.753
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.202	C=0.798
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.301	C=0.699
Allele Frequency Aggregator	Asian	Sub	112	G=0.188	C=0.812
Allele Frequency Aggregator	South Asian	Sub	98	G=0.31	C=0.69
8.3KJPN	JAPANESE	Study-wide	16758	G=0.15563	C=0.84437
1000Genomes_30x	Global	Study-wide	6404	G=0.2038	C=0.7962
1000Genomes_30x	African	Sub	1786	G=0.1170	C=0.8830
1000Genomes_30x	Europe	Sub	1266	G=0.2915	C=0.7085
1000Genomes_30x	South Asian	Sub	1202	G=0.2654	C=0.7346
1000Genomes_30x	East Asian	Sub	1170	G=0.1556	C=0.8444
1000Genomes_30x	American	Sub	980	G=0.231	C=0.769
1000Genomes	Global	Study-wide	5008	G=0.2037	C=0.7963
1000Genomes	African	Sub	1322	G=0.1180	C=0.8820
1000Genomes	East Asian	Sub	1008	G=0.1548	C=0.8452
1000Genomes	Europe	Sub	1006	G=0.2962	C=0.7038
1000Genomes	South Asian	Sub	978	G=0.261	C=0.739
1000Genomes	American	Sub	694	G=0.223	C=0.777
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.2462	C=0.7538
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.2769	C=0.7231
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.2743	C=0.7257
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.1611	C=0.8389
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.296	C=0.704
Northern Sweden	ACPOP	Study-wide	600	G=0.218	C=0.782
SGDP_PRJ	Global	Study-wide	522	G=0.182	C=0.818
HapMap	Global	Study-wide	304	G=0.095	C=0.905
HapMap	African	Sub	108	G=0.083	C=0.917
HapMap	American	Sub	108	G=0.139	C=0.861
HapMap	Asian	Sub	88	G=0.06	C=0.94
Qatari	Global	Study-wide	216	G=0.245	C=0.755
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.099	C=0.901
Siberian	Global	Study-wide	54	G=0.11	C=0.89
The Danish reference pan genome	Danish	Study-wide	40	G=0.20	C=0.80

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 22	NC_000022.11:g.36650714G>C
GRCh37.p13 chr 22	NC_000022.10:g.37046761G>C
CACNG2 RefSeqGene (LRG_1159)	NG_031861.2:g.57145C>G

Gene: CACNG2, calcium voltage-gated channel auxiliary subunit gamma 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNG2 transcript variant 2	NM_001379051.1:c.142+5165… NM_001379051.1:c.142+51652C>G	N/A	Intron Variant
CACNG2 transcript variant 1	NM_006078.5:c.211+51652C>G	N/A	Intron Variant
CACNG2 transcript variant 3	NR_166440.1:n.	N/A	Intron Variant
CACNG2 transcript variant X1	XM_017028531.3: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	G=	C
GRCh38.p14 chr 22	NC_000022.11:g.36650714=	NC_000022.11:g.36650714G>C
GRCh37.p13 chr 22	NC_000022.10:g.37046761=	NC_000022.10:g.37046761G>C
CACNG2 RefSeqGene (LRG_1159)	NG_031861.2:g.57145=	NG_031861.2:g.57145C>G
CACNG2 transcript variant 2	NM_001379051.1:c.142+51652=	NM_001379051.1:c.142+51652C>G
CACNG2 transcript	NM_006078.3:c.211+51650=	NM_006078.3:c.211+51650C>G
CACNG2 transcript variant 1	NM_006078.5:c.211+51652=	NM_006078.5:c.211+51652C>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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC	ss139536	Jun 24, 2000 (78)
2	SC_SNP	ss8007067	Apr 21, 2003 (123)
3	SC_SNP	ss13349980	Dec 05, 2003 (123)
4	CSHL-HAPMAP	ss17723256	Feb 27, 2004 (123)
5	CSHL-HAPMAP	ss19503787	Feb 27, 2004 (123)
6	SSAHASNP	ss21860001	Apr 05, 2004 (123)
7	ABI	ss41522246	Mar 14, 2006 (126)
8	BCMHGSC_JDW	ss91920468	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss96100580	Feb 05, 2009 (130)
10	BGI	ss106226660	Feb 05, 2009 (130)
11	1000GENOMES	ss114205414	Jan 25, 2009 (130)
12	ILLUMINA-UK	ss117403839	Dec 01, 2009 (131)
13	ENSEMBL	ss138354979	Dec 01, 2009 (131)
14	ENSEMBL	ss143708994	Dec 01, 2009 (131)
15	GMI	ss157176164	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss167937863	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss169243944	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss171972886	Jul 04, 2010 (132)
19	BUSHMAN	ss204088371	Jul 04, 2010 (132)
20	1000GENOMES	ss210977004	Jul 14, 2010 (132)
21	1000GENOMES	ss228680770	Jul 14, 2010 (132)
22	1000GENOMES	ss238070259	Jul 15, 2010 (132)
23	1000GENOMES	ss244187964	Jul 15, 2010 (132)
24	BL	ss255901585	May 09, 2011 (134)
25	GMI	ss283636749	May 04, 2012 (137)
26	GMI	ss287569534	Apr 25, 2013 (138)
27	PJP	ss292761235	May 09, 2011 (134)
28	TISHKOFF	ss566642534	Apr 25, 2013 (138)
29	SSMP	ss662572694	Apr 25, 2013 (138)
30	EVA-GONL	ss995355664	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1082661397	Aug 21, 2014 (142)
32	1000GENOMES	ss1367178936	Aug 21, 2014 (142)
33	DDI	ss1429257737	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1579754405	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1640002546	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1682996579	Apr 01, 2015 (144)
37	EVA_DECODE	ss1699425746	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1809790419	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1938922258	Feb 12, 2016 (147)
40	GENOMED	ss1969273396	Jul 19, 2016 (147)
41	JJLAB	ss2030233167	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2158852237	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2247359224	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2629613856	Nov 08, 2017 (151)
45	GRF	ss2704604192	Nov 08, 2017 (151)
46	GNOMAD	ss2974424463	Nov 08, 2017 (151)
47	SWEGEN	ss3019310172	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3028953806	Nov 08, 2017 (151)
49	CSHL	ss3352839722	Nov 08, 2017 (151)
50	URBANLAB	ss3651180401	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3685805732	Jul 13, 2019 (153)
52	EVA_DECODE	ss3708208432	Jul 13, 2019 (153)
53	ACPOP	ss3743938062	Jul 13, 2019 (153)
54	EVA	ss3759387858	Jul 13, 2019 (153)
55	PACBIO	ss3788827840	Jul 13, 2019 (153)
56	PACBIO	ss3793693294	Jul 13, 2019 (153)
57	PACBIO	ss3798579760	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3822550889	Jul 13, 2019 (153)
59	EVA	ss3835994268	Apr 27, 2020 (154)
60	SGDP_PRJ	ss3890554225	Apr 27, 2020 (154)
61	KRGDB	ss3940952695	Apr 27, 2020 (154)
62	TOPMED	ss5109345785	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5232644121	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5311114766	Oct 16, 2022 (156)
65	HUGCELL_USP	ss5502955580	Oct 16, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5618676612	Oct 16, 2022 (156)
67	SANFORD_IMAGENETICS	ss5664501727	Oct 16, 2022 (156)
68	TOMMO_GENOMICS	ss5793769587	Oct 16, 2022 (156)
69	YY_MCH	ss5818716585	Oct 16, 2022 (156)
70	EVA	ss5822078328	Oct 16, 2022 (156)
71	EVA	ss5853396092	Oct 16, 2022 (156)
72	EVA	ss5881837223	Oct 16, 2022 (156)
73	EVA	ss5959357546	Oct 16, 2022 (156)
74	EVA	ss5981135535	Oct 16, 2022 (156)
75	1000Genomes	NC_000022.10 - 37046761	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000022.11 - 36650714	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 37046761	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000022.10 - 37046761	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000022.10 - 37046761	Apr 27, 2020 (154)
80	gnomAD - Genomes	NC_000022.11 - 36650714	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000022.10 - 37046761	Apr 27, 2020 (154)
82	HapMap	NC_000022.11 - 36650714	Apr 27, 2020 (154)
83	KOREAN population from KRGDB	NC_000022.10 - 37046761	Apr 27, 2020 (154)
84	Northern Sweden	NC_000022.10 - 37046761	Jul 13, 2019 (153)
85	Qatari	NC_000022.10 - 37046761	Apr 27, 2020 (154)
86	SGDP_PRJ	NC_000022.10 - 37046761	Apr 27, 2020 (154)
87	Siberian	NC_000022.10 - 37046761	Apr 27, 2020 (154)
88	8.3KJPN	NC_000022.10 - 37046761	Apr 26, 2021 (155)
89	14KJPN	NC_000022.11 - 36650714	Oct 16, 2022 (156)
90	TopMed	NC_000022.11 - 36650714	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000022.10 - 37046761	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000022.10 - 37046761	Jul 13, 2019 (153)
93	ALFA	NC_000022.11 - 36650714	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)
rs5756279	Sep 24, 2004 (123)
rs9607364	Sep 24, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss91920468, ss114205414, ss117403839, ss167937863, ss169243944, ss171972886, ss204088371, ss210977004, ss255901585, ss283636749, ss287569534, ss292761235, ss1699425746	NC_000022.9:35376706:G:C	NC_000022.11:36650713:G:C	(self)
80731631, 44657841, 31543980, 5919344, 19900095, 48130089, 17222927, 20964180, 42571205, 11368591, 90613428, 44657841, 9852435, ss228680770, ss238070259, ss244187964, ss566642534, ss662572694, ss995355664, ss1082661397, ss1367178936, ss1429257737, ss1579754405, ss1640002546, ss1682996579, ss1809790419, ss1938922258, ss1969273396, ss2030233167, ss2158852237, ss2629613856, ss2704604192, ss2974424463, ss3019310172, ss3352839722, ss3685805732, ss3743938062, ss3759387858, ss3788827840, ss3793693294, ss3798579760, ss3835994268, ss3890554225, ss3940952695, ss5232644121, ss5664501727, ss5822078328, ss5959357546, ss5981135535	NC_000022.10:37046760:G:C	NC_000022.11:36650713:G:C	(self)
106202547, 570080700, 2256642, 127606691, 384454732, 11493728765, ss2247359224, ss3028953806, ss3651180401, ss3708208432, ss3822550889, ss5109345785, ss5311114766, ss5502955580, ss5618676612, ss5793769587, ss5818716585, ss5853396092, ss5881837223	NC_000022.11:36650713:G:C	NC_000022.11:36650713:G:C	(self)
ss13349980, ss17723256, ss19503787, ss21860001	NT_011520.9:16355814:G:C	NC_000022.11:36650713:G:C	(self)
ss139536, ss8007067, ss41522246, ss96100580, ss106226660, ss138354979, ss143708994, ss157176164	NT_011520.12:16437329:G:C	NC_000022.11:36650713:G:C	(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 rs131825

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

rs131825