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dbSNP Short Genetic Variations

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.

rs147629240

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:181481989 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000638 (169/264690, TOPMED)
T=0.000813 (114/140234, GnomAD)
T=0.00083 (12/14420, ALFA) (+ 4 more)
T=0.0011 (7/6404, 1000G_30x)
T=0.0010 (5/5008, 1000G)
T=0.0016 (6/3854, ALSPAC)
T=0.0016 (6/3708, TWINSUK)
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 14420 C=0.99917 T=0.00083
European Sub 9824 C=0.9989 T=0.0011
African Sub 2946 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2832 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.993 T=0.007
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 684 C=1.000 T=0.000


Help

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 C=0.999362 T=0.000638
gnomAD - Genomes Global Study-wide 140234 C=0.999187 T=0.000813
gnomAD - Genomes European Sub 75928 C=0.99905 T=0.00095
gnomAD - Genomes African Sub 42036 C=0.99957 T=0.00043
gnomAD - Genomes American Sub 13664 C=0.99839 T=0.00161
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9991 T=0.0009
Allele Frequency Aggregator Total Global 14420 C=0.99917 T=0.00083
Allele Frequency Aggregator European Sub 9824 C=0.9989 T=0.0011
Allele Frequency Aggregator African Sub 2946 C=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 684 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.993 T=0.007
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9989 T=0.0011
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9953 T=0.0047
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.999 T=0.001
1000Genomes Global Study-wide 5008 C=0.9990 T=0.0010
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9960 T=0.0040
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.999 T=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9984 T=0.0016
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9984 T=0.0016
Help

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.181481989C>T
GRCh37.p13 chr 1 NC_000001.10:g.181451125C>T
CACNA1E RefSeqGene NG_050616.1:g.3679C>T
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. N/A Genic Upstream Transcript Variant
CACNA1E transcript variant 1 NM_001205293.3:c. N/A Genic Upstream Transcript Variant
CACNA1E transcript variant 2 NM_001205294.2:c. N/A Genic Upstream Transcript Variant
CACNA1E transcript variant X1 XM_017002243.2:c.435-1755…

XM_017002243.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X2 XM_017002244.2:c.435-1755…

XM_017002244.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X3 XM_017002245.2:c.435-1755…

XM_017002245.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X4 XM_017002246.2:c.435-1755…

XM_017002246.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X5 XM_017002247.2:c.435-1755…

XM_017002247.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X6 XM_017002248.2:c.435-1755…

XM_017002248.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X8 XM_017002249.2:c.435-1755…

XM_017002249.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X9 XM_017002250.2:c.435-1755…

XM_017002250.2:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X10 XM_017002251.1:c.435-1755…

XM_017002251.1:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X7 XM_047429979.1:c.435-1755…

XM_047429979.1:c.435-1755C>T

N/A Intron Variant
CACNA1E transcript variant X11 XM_047429980.1:c.435-1755…

XM_047429980.1:c.435-1755C>T

N/A Intron Variant
Help

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
Help

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 C= T
GRCh38.p14 chr 1 NC_000001.11:g.181481989= NC_000001.11:g.181481989C>T
GRCh37.p13 chr 1 NC_000001.10:g.181451125= NC_000001.10:g.181451125C>T
CACNA1E RefSeqGene NG_050616.1:g.3679= NG_050616.1:g.3679C>T
CACNA1E transcript variant X1 XM_017002243.2:c.435-1755= XM_017002243.2:c.435-1755C>T
CACNA1E transcript variant X2 XM_017002244.2:c.435-1755= XM_017002244.2:c.435-1755C>T
CACNA1E transcript variant X3 XM_017002245.2:c.435-1755= XM_017002245.2:c.435-1755C>T
CACNA1E transcript variant X4 XM_017002246.2:c.435-1755= XM_017002246.2:c.435-1755C>T
CACNA1E transcript variant X5 XM_017002247.2:c.435-1755= XM_017002247.2:c.435-1755C>T
CACNA1E transcript variant X6 XM_017002248.2:c.435-1755= XM_017002248.2:c.435-1755C>T
CACNA1E transcript variant X8 XM_017002249.2:c.435-1755= XM_017002249.2:c.435-1755C>T
CACNA1E transcript variant X9 XM_017002250.2:c.435-1755= XM_017002250.2:c.435-1755C>T
CACNA1E transcript variant X10 XM_017002251.1:c.435-1755= XM_017002251.1:c.435-1755C>T
CACNA1E transcript variant X7 XM_047429979.1:c.435-1755= XM_047429979.1:c.435-1755C>T
CACNA1E transcript variant X11 XM_047429980.1:c.435-1755= XM_047429980.1:c.435-1755C>T
Help

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#.

17 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss329069088 May 09, 2011 (134)
2 1000GENOMES ss1293670277 Aug 21, 2014 (142)
3 EVA_DECODE ss1585268270 Apr 01, 2015 (144)
4 EVA_UK10K_ALSPAC ss1601612314 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1644606347 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2168062615 Dec 20, 2016 (150)
7 GNOMAD ss2763426249 Nov 08, 2017 (151)
8 SWEGEN ss2988052009 Nov 08, 2017 (151)
9 EVA_DECODE ss3688144855 Jul 12, 2019 (153)
10 TOPMED ss4474870147 Apr 25, 2021 (155)
11 1000G_HIGH_COVERAGE ss5244937718 Oct 12, 2022 (156)
12 EVA ss5323229654 Oct 12, 2022 (156)
13 HUGCELL_USP ss5445458250 Oct 12, 2022 (156)
14 1000G_HIGH_COVERAGE ss5518591236 Oct 12, 2022 (156)
15 SANFORD_IMAGENETICS ss5626959347 Oct 12, 2022 (156)
16 EVA ss5910988018 Oct 12, 2022 (156)
17 EVA ss5938772396 Oct 12, 2022 (156)
18 1000Genomes NC_000001.10 - 181451125 Oct 11, 2018 (152)
19 1000Genomes_30x NC_000001.11 - 181481989 Oct 12, 2022 (156)
20 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 181451125 Oct 11, 2018 (152)
21 gnomAD - Genomes NC_000001.11 - 181481989 Apr 25, 2021 (155)
22 TopMed NC_000001.11 - 181481989 Apr 25, 2021 (155)
23 UK 10K study - Twins NC_000001.10 - 181451125 Oct 11, 2018 (152)
24 ALFA NC_000001.11 - 181481989 Apr 25, 2021 (155)
Help

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
ss1585268270 NC_000001.9:179717747:C:T NC_000001.11:181481988:C:T (self)
4488407, 2458456, 2458456, ss329069088, ss1293670277, ss1601612314, ss1644606347, ss2763426249, ss2988052009, ss5323229654, ss5626959347, ss5938772396 NC_000001.10:181451124:C:T NC_000001.11:181481988:C:T (self)
6117171, 32419608, 38476482, 5400811993, ss2168062615, ss3688144855, ss4474870147, ss5244937718, ss5445458250, ss5518591236, ss5910988018 NC_000001.11:181481988:C:T NC_000001.11:181481988:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs147629240

Help

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.

Software version is: 2.0.1.post761+d5e8e07