Name: rs147188122
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.

rs147188122

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:13343022 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.123945 (32807/264690, TOPMED)
C=0.116583 (16330/140072, GnomAD)
C=0.29553 (8351/28258, 14KJPN) (+ 13 more)
C=0.09307 (1758/18890, ALFA)
C=0.29553 (4953/16760, 8.3KJPN)
C=0.1854 (1187/6404, 1000G_30x)
C=0.1911 (957/5008, 1000G)
C=0.0632 (283/4480, Estonian)
C=0.0698 (269/3854, ALSPAC)
C=0.0725 (269/3708, TWINSUK)
C=0.3693 (1082/2930, KOREAN)
C=0.079 (79/998, GoNL)
C=0.055 (33/600, NorthernSweden)
C=0.162 (35/216, Qatari)
T=0.442 (76/172, SGDP_PRJ)
T=0.44 (8/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CACNA1A : 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	T=0.90693	C=0.09307
European	Sub	14286	T=0.92839	C=0.07161
African	Sub	2946	T=0.8184	C=0.1816
African Others	Sub	114	T=0.842	C=0.158
African American	Sub	2832	T=0.8174	C=0.1826
Asian	Sub	112	T=0.696	C=0.304
East Asian	Sub	86	T=0.67	C=0.33
Other Asian	Sub	26	T=0.77	C=0.23
Latin American 1	Sub	146	T=0.842	C=0.158
Latin American 2	Sub	610	T=0.915	C=0.085
South Asian	Sub	98	T=0.80	C=0.20
Other	Sub	692	T=0.897	C=0.103

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=0.876055	C=0.123945
gnomAD - Genomes	Global	Study-wide	140072	T=0.883417	C=0.116583
gnomAD - Genomes	European	Sub	75886	T=0.92456	C=0.07544
gnomAD - Genomes	African	Sub	41954	T=0.81668	C=0.18332
gnomAD - Genomes	American	Sub	13640	T=0.91957	C=0.08043
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.8813	C=0.1187
gnomAD - Genomes	East Asian	Sub	3122	T=0.6268	C=0.3732
gnomAD - Genomes	Other	Sub	2150	T=0.8800	C=0.1200
14KJPN	JAPANESE	Study-wide	28258	T=0.70447	C=0.29553
Allele Frequency Aggregator	Total	Global	18890	T=0.90693	C=0.09307
Allele Frequency Aggregator	European	Sub	14286	T=0.92839	C=0.07161
Allele Frequency Aggregator	African	Sub	2946	T=0.8184	C=0.1816
Allele Frequency Aggregator	Other	Sub	692	T=0.897	C=0.103
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.915	C=0.085
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.842	C=0.158
Allele Frequency Aggregator	Asian	Sub	112	T=0.696	C=0.304
Allele Frequency Aggregator	South Asian	Sub	98	T=0.80	C=0.20
8.3KJPN	JAPANESE	Study-wide	16760	T=0.70447	C=0.29553
1000Genomes_30x	Global	Study-wide	6404	T=0.8146	C=0.1854
1000Genomes_30x	African	Sub	1786	T=0.8130	C=0.1870
1000Genomes_30x	Europe	Sub	1266	T=0.9289	C=0.0711
1000Genomes_30x	South Asian	Sub	1202	T=0.7987	C=0.2013
1000Genomes_30x	East Asian	Sub	1170	T=0.6274	C=0.3726
1000Genomes_30x	American	Sub	980	T=0.913	C=0.087
1000Genomes	Global	Study-wide	5008	T=0.8089	C=0.1911
1000Genomes	African	Sub	1322	T=0.8132	C=0.1868
1000Genomes	East Asian	Sub	1008	T=0.6290	C=0.3710
1000Genomes	Europe	Sub	1006	T=0.9215	C=0.0785
1000Genomes	South Asian	Sub	978	T=0.806	C=0.194
1000Genomes	American	Sub	694	T=0.903	C=0.097
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9368	C=0.0632
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9302	C=0.0698
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9275	C=0.0725
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.6307	C=0.3693
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.921	C=0.079
Northern Sweden	ACPOP	Study-wide	600	T=0.945	C=0.055
Qatari	Global	Study-wide	216	T=0.838	C=0.162
SGDP_PRJ	Global	Study-wide	172	T=0.442	C=0.558
Siberian	Global	Study-wide	18	T=0.44	C=0.56

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 19	NC_000019.10:g.13343022T>C
GRCh37.p13 chr 19	NC_000019.9:g.13453836T>C
CACNA1A RefSeqGene (LRG_7)	NG_011569.1:g.168439A>G

Gene: CACNA1A, calcium voltage-gated channel subunit alpha1 A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA1A transcript variant 1	NM_000068.4:c.979-7113A>G	N/A	Intron Variant
CACNA1A transcript variant 3	NM_001127221.2:c.979-7113… NM_001127221.2:c.979-7113A>G	N/A	Intron Variant
CACNA1A transcript variant 4	NM_001127222.2:c.979-7113… NM_001127222.2:c.979-7113A>G	N/A	Intron Variant
CACNA1A transcript variant 5	NM_001174080.2:c.979-7113… NM_001174080.2:c.979-7113A>G	N/A	Intron Variant
CACNA1A transcript variant 2	NM_023035.3:c.979-7113A>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=	C
GRCh38.p14 chr 19	NC_000019.10:g.13343022=	NC_000019.10:g.13343022T>C
GRCh37.p13 chr 19	NC_000019.9:g.13453836=	NC_000019.9:g.13453836T>C
CACNA1A RefSeqGene (LRG_7)	NG_011569.1:g.168439=	NG_011569.1:g.168439A>G
CACNA1A transcript variant 1	NM_000068.3:c.979-7113=	NM_000068.3:c.979-7113A>G
CACNA1A transcript variant 1	NM_000068.4:c.979-7113=	NM_000068.4:c.979-7113A>G
CACNA1A transcript variant 3	NM_001127221.1:c.979-7113=	NM_001127221.1:c.979-7113A>G
CACNA1A transcript variant 3	NM_001127221.2:c.979-7113=	NM_001127221.2:c.979-7113A>G
CACNA1A transcript variant 4	NM_001127222.1:c.979-7113=	NM_001127222.1:c.979-7113A>G
CACNA1A transcript variant 4	NM_001127222.2:c.979-7113=	NM_001127222.2:c.979-7113A>G
CACNA1A transcript variant 5	NM_001174080.1:c.979-7113=	NM_001174080.1:c.979-7113A>G
CACNA1A transcript variant 5	NM_001174080.2:c.979-7113=	NM_001174080.2:c.979-7113A>G
CACNA1A transcript variant 2	NM_023035.2:c.979-7113=	NM_023035.2:c.979-7113A>G
CACNA1A transcript variant 2	NM_023035.3:c.979-7113=	NM_023035.3:c.979-7113A>G
CACNA1A transcript variant X1	XM_005260065.1:c.979-7113=	XM_005260065.1:c.979-7113A>G
CACNA1A transcript variant X2	XM_005260066.1:c.979-7113=	XM_005260066.1:c.979-7113A>G
CACNA1A transcript variant X3	XM_005260067.1:c.979-7113=	XM_005260067.1:c.979-7113A>G
CACNA1A transcript variant X4	XM_005260068.1:c.979-7113=	XM_005260068.1:c.979-7113A>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#.

41 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss340334363	May 09, 2011 (134)
2	GMI	ss475841806	May 04, 2012 (137)
3	TISHKOFF	ss565865891	Apr 25, 2013 (138)
4	SSMP	ss661722343	Apr 25, 2013 (138)
5	EVA-GONL	ss994108701	Aug 21, 2014 (142)
6	JMKIDD_LAB	ss1081771241	Aug 21, 2014 (142)
7	1000GENOMES	ss1362436558	Aug 21, 2014 (142)
8	DDI	ss1428341400	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1637604680	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1680598713	Apr 01, 2015 (144)
11	EVA_DECODE	ss1698168392	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1937593216	Feb 12, 2016 (147)
13	JJLAB	ss2029568446	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2158093750	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2224461403	Dec 20, 2016 (150)
16	SYSTEMSBIOZJU	ss2629283460	Nov 08, 2017 (151)
17	GRF	ss2702698254	Nov 08, 2017 (151)
18	GNOMAD	ss2960716478	Nov 08, 2017 (151)
19	SWEGEN	ss3017137315	Nov 08, 2017 (151)
20	EGCUT_WGS	ss3683964543	Jul 13, 2019 (153)
21	EVA_DECODE	ss3702388786	Jul 13, 2019 (153)
22	ACPOP	ss3742873291	Jul 13, 2019 (153)
23	EVA	ss3755836426	Jul 13, 2019 (153)
24	KHV_HUMAN_GENOMES	ss3821091086	Jul 13, 2019 (153)
25	EVA	ss3835362407	Apr 27, 2020 (154)
26	SGDP_PRJ	ss3887812831	Apr 27, 2020 (154)
27	KRGDB	ss3937796063	Apr 27, 2020 (154)
28	TOPMED	ss5068697491	Apr 27, 2021 (155)
29	TOMMO_GENOMICS	ss5226854653	Apr 27, 2021 (155)
30	1000G_HIGH_COVERAGE	ss5306575864	Oct 16, 2022 (156)
31	EVA	ss5433702798	Oct 16, 2022 (156)
32	HUGCELL_USP	ss5499193096	Oct 16, 2022 (156)
33	EVA	ss5512044420	Oct 16, 2022 (156)
34	1000G_HIGH_COVERAGE	ss5612007110	Oct 16, 2022 (156)
35	SANFORD_IMAGENETICS	ss5662019854	Oct 16, 2022 (156)
36	TOMMO_GENOMICS	ss5785174493	Oct 16, 2022 (156)
37	YY_MCH	ss5817426628	Oct 16, 2022 (156)
38	EVA	ss5840285694	Oct 16, 2022 (156)
39	EVA	ss5852212728	Oct 16, 2022 (156)
40	EVA	ss5927382108	Oct 16, 2022 (156)
41	EVA	ss5953440278	Oct 16, 2022 (156)
42	1000Genomes	NC_000019.9 - 13453836	Oct 12, 2018 (152)
43	1000Genomes_30x	NC_000019.10 - 13343022	Oct 16, 2022 (156)
44	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 13453836	Oct 12, 2018 (152)
45	Genetic variation in the Estonian population	NC_000019.9 - 13453836	Oct 12, 2018 (152)
46	gnomAD - Genomes	NC_000019.10 - 13343022	Apr 27, 2021 (155)
47	Genome of the Netherlands Release 5	NC_000019.9 - 13453836	Apr 27, 2020 (154)
48	KOREAN population from KRGDB	NC_000019.9 - 13453836	Apr 27, 2020 (154)
49	Northern Sweden	NC_000019.9 - 13453836	Jul 13, 2019 (153)
50	Qatari	NC_000019.9 - 13453836	Apr 27, 2020 (154)
51	SGDP_PRJ	NC_000019.9 - 13453836	Apr 27, 2020 (154)
52	Siberian	NC_000019.9 - 13453836	Apr 27, 2020 (154)
53	8.3KJPN	NC_000019.9 - 13453836	Apr 27, 2021 (155)
54	14KJPN	NC_000019.10 - 13343022	Oct 16, 2022 (156)
55	TopMed	NC_000019.10 - 13343022	Apr 27, 2021 (155)
56	UK 10K study - Twins	NC_000019.9 - 13453836	Oct 12, 2018 (152)
57	ALFA	NC_000019.10 - 13343022	Apr 27, 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
ss475841806, ss1698168392	NC_000019.8:13314835:T:C	NC_000019.10:13343021:T:C	(self)
75817228, 42005477, 29702791, 18712994, 44973457, 16158156, 19635138, 39829811, 10610104, 84823960, 42005477, ss340334363, ss565865891, ss661722343, ss994108701, ss1081771241, ss1362436558, ss1428341400, ss1637604680, ss1680598713, ss1937593216, ss2029568446, ss2158093750, ss2629283460, ss2702698254, ss2960716478, ss3017137315, ss3683964543, ss3742873291, ss3755836426, ss3835362407, ss3887812831, ss3937796063, ss5226854653, ss5433702798, ss5512044420, ss5662019854, ss5840285694, ss5953440278	NC_000019.9:13453835:T:C	NC_000019.10:13343021:T:C	(self)
99533045, 534713350, 119011597, 284243155, 5089929444, ss2224461403, ss3702388786, ss3821091086, ss5068697491, ss5306575864, ss5499193096, ss5612007110, ss5785174493, ss5817426628, ss5852212728, ss5927382108	NC_000019.10:13343021:T:C	NC_000019.10:13343021:T: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 rs147188122

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

rs147188122