Name: rs72770908
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.

rs72770908

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:138112204 (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=0.141581 (37475/264690, TOPMED)
A=0.136200 (19080/140088, GnomAD)
A=0.13954 (4306/30858, ALFA) (+ 17 more)
A=0.30045 (8490/28258, 14KJPN)
A=0.29916 (5014/16760, 8.3KJPN)
A=0.1683 (1078/6404, 1000G_30x)
A=0.1743 (873/5008, 1000G)
A=0.0996 (446/4478, Estonian)
A=0.1474 (568/3854, ALSPAC)
A=0.1435 (532/3708, TWINSUK)
A=0.3171 (929/2930, KOREAN)
A=0.3204 (587/1832, Korea1K)
A=0.132 (132/998, GoNL)
A=0.100 (60/600, NorthernSweden)
A=0.007 (4/534, MGP)
A=0.157 (34/216, Qatari)
G=0.430 (74/172, SGDP_PRJ)
A=0.15 (6/40, GENOME_DK)
G=0.50 (7/14, Siberian)
A=0.50 (7/14, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CACNA1B : 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	30858	G=0.86046	A=0.13954
European	Sub	24728	G=0.86141	A=0.13859
African	Sub	3168	G=0.8589	A=0.1411
African Others	Sub	124	G=0.782	A=0.218
African American	Sub	3044	G=0.8620	A=0.1380
Asian	Sub	128	G=0.688	A=0.312
East Asian	Sub	100	G=0.72	A=0.28
Other Asian	Sub	28	G=0.57	A=0.43
Latin American 1	Sub	168	G=0.869	A=0.131
Latin American 2	Sub	700	G=0.913	A=0.087
South Asian	Sub	114	G=0.798	A=0.202
Other	Sub	1852	G=0.8456	A=0.1544

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=0.858419	A=0.141581
gnomAD - Genomes	Global	Study-wide	140088	G=0.863800	A=0.136200
gnomAD - Genomes	European	Sub	75882	G=0.86884	A=0.13116
gnomAD - Genomes	African	Sub	41974	G=0.86318	A=0.13682
gnomAD - Genomes	American	Sub	13638	G=0.89067	A=0.10933
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.8293	A=0.1707
gnomAD - Genomes	East Asian	Sub	3120	G=0.6788	A=0.3212
gnomAD - Genomes	Other	Sub	2152	G=0.8494	A=0.1506
Allele Frequency Aggregator	Total	Global	30858	G=0.86046	A=0.13954
Allele Frequency Aggregator	European	Sub	24728	G=0.86141	A=0.13859
Allele Frequency Aggregator	African	Sub	3168	G=0.8589	A=0.1411
Allele Frequency Aggregator	Other	Sub	1852	G=0.8456	A=0.1544
Allele Frequency Aggregator	Latin American 2	Sub	700	G=0.913	A=0.087
Allele Frequency Aggregator	Latin American 1	Sub	168	G=0.869	A=0.131
Allele Frequency Aggregator	Asian	Sub	128	G=0.688	A=0.312
Allele Frequency Aggregator	South Asian	Sub	114	G=0.798	A=0.202
14KJPN	JAPANESE	Study-wide	28258	G=0.69955	A=0.30045
8.3KJPN	JAPANESE	Study-wide	16760	G=0.70084	A=0.29916
1000Genomes_30x	Global	Study-wide	6404	G=0.8317	A=0.1683
1000Genomes_30x	African	Sub	1786	G=0.8802	A=0.1198
1000Genomes_30x	Europe	Sub	1266	G=0.8815	A=0.1185
1000Genomes_30x	South Asian	Sub	1202	G=0.7812	A=0.2188
1000Genomes_30x	East Asian	Sub	1170	G=0.6769	A=0.3231
1000Genomes_30x	American	Sub	980	G=0.926	A=0.074
1000Genomes	Global	Study-wide	5008	G=0.8257	A=0.1743
1000Genomes	African	Sub	1322	G=0.8775	A=0.1225
1000Genomes	East Asian	Sub	1008	G=0.6766	A=0.3234
1000Genomes	Europe	Sub	1006	G=0.8877	A=0.1123
1000Genomes	South Asian	Sub	978	G=0.778	A=0.222
1000Genomes	American	Sub	694	G=0.921	A=0.079
Genetic variation in the Estonian population	Estonian	Study-wide	4478	G=0.9004	A=0.0996
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8526	A=0.1474
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8565	A=0.1435
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.6829	A=0.3171
Korean Genome Project	KOREAN	Study-wide	1832	G=0.6796	A=0.3204
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.868	A=0.132
Northern Sweden	ACPOP	Study-wide	600	G=0.900	A=0.100
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.993	A=0.007
Qatari	Global	Study-wide	216	G=0.843	A=0.157
SGDP_PRJ	Global	Study-wide	172	G=0.430	A=0.570
The Danish reference pan genome	Danish	Study-wide	40	G=0.85	A=0.15
Siberian	Global	Study-wide	14	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 9	NC_000009.12:g.138112204G>A
GRCh37.p13 chr 9	NC_000009.11:g.141006656G>A
CACNA1B RefSeqGene	NG_042271.1:g.239416G>A

Gene: CACNA1B, calcium voltage-gated channel subunit alpha1 B (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA1B transcript variant 1	NM_000718.4:c.5429-194G>A	N/A	Intron Variant
CACNA1B transcript variant 2	NM_001243812.2:c.5429-194… NM_001243812.2:c.5429-194G>A	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.

Allele: A (allele ID: 1222153 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001616951.3	not provided	Benign

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 9	NC_000009.12:g.138112204=	NC_000009.12:g.138112204G>A
GRCh37.p13 chr 9	NC_000009.11:g.141006656=	NC_000009.11:g.141006656G>A
CACNA1B RefSeqGene	NG_042271.1:g.239416=	NG_042271.1:g.239416G>A
CACNA1B transcript variant 1	NM_000718.3:c.5429-194=	NM_000718.3:c.5429-194G>A
CACNA1B transcript variant 1	NM_000718.4:c.5429-194=	NM_000718.4:c.5429-194G>A
CACNA1B transcript variant 2	NM_001243812.1:c.5429-194=	NM_001243812.1:c.5429-194G>A
CACNA1B transcript variant 2	NM_001243812.2:c.5429-194=	NM_001243812.2:c.5429-194G>A
CACNA1B transcript variant X1	XM_005266103.1:c.5435-194=	XM_005266103.1:c.5435-194G>A
CACNA1B transcript variant X2	XM_005266104.1:c.5426-194=	XM_005266104.1:c.5426-194G>A

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#.

63 SubSNP, 19 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	BGI	ss104662903	Dec 01, 2009 (131)
2	1000GENOMES	ss109145497	Feb 13, 2009 (130)
3	GMI	ss158075411	Dec 01, 2009 (131)
4	1000GENOMES	ss224511991	Jul 14, 2010 (132)
5	1000GENOMES	ss235011911	Jul 15, 2010 (132)
6	1000GENOMES	ss241753010	Jul 15, 2010 (132)
7	GMI	ss280439369	May 04, 2012 (137)
8	ILLUMINA	ss484100932	May 04, 2012 (137)
9	ILLUMINA	ss485752096	May 04, 2012 (137)
10	ILLUMINA	ss536291177	Sep 08, 2015 (146)
11	TISHKOFF	ss561707608	Apr 25, 2013 (138)
12	SSMP	ss656206435	Apr 25, 2013 (138)
13	ILLUMINA	ss780526750	Sep 08, 2015 (146)
14	ILLUMINA	ss782495603	Sep 08, 2015 (146)
15	ILLUMINA	ss836018284	Sep 08, 2015 (146)
16	EVA-GONL	ss987095642	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1076687156	Aug 21, 2014 (142)
18	1000GENOMES	ss1335908209	Aug 21, 2014 (142)
19	EVA_GENOME_DK	ss1583300717	Apr 01, 2015 (144)
20	EVA_DECODE	ss1596743554	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1623796908	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1666790941	Apr 01, 2015 (144)
23	EVA_MGP	ss1711244973	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1930412909	Feb 12, 2016 (147)
25	JJLAB	ss2025929012	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2154168811	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2315370690	Dec 20, 2016 (150)
28	SYSTEMSBIOZJU	ss2627432384	Nov 08, 2017 (151)
29	ILLUMINA	ss2634932422	Nov 08, 2017 (151)
30	GRF	ss2710054661	Nov 08, 2017 (151)
31	GNOMAD	ss2884496885	Nov 08, 2017 (151)
32	AFFY	ss2986125308	Nov 08, 2017 (151)
33	SWEGEN	ss3005778895	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3026746583	Nov 08, 2017 (151)
35	CSHL	ss3348910179	Nov 08, 2017 (151)
36	ILLUMINA	ss3630385024	Oct 12, 2018 (152)
37	ILLUMINA	ss3632820120	Oct 12, 2018 (152)
38	ILLUMINA	ss3642719826	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3673314598	Jul 13, 2019 (153)
40	EVA_DECODE	ss3724986572	Jul 13, 2019 (153)
41	ACPOP	ss3736973246	Jul 13, 2019 (153)
42	EVA	ss3769833965	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3812991916	Jul 13, 2019 (153)
44	EVA	ss3831916395	Apr 26, 2020 (154)
45	EVA	ss3839486873	Apr 26, 2020 (154)
46	EVA	ss3844952318	Apr 26, 2020 (154)
47	SGDP_PRJ	ss3873321413	Apr 26, 2020 (154)
48	KRGDB	ss3921244911	Apr 26, 2020 (154)
49	KOGIC	ss3967018008	Apr 26, 2020 (154)
50	TOPMED	ss4839490952	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5195838989	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5282589424	Oct 16, 2022 (156)
53	EVA	ss5315442422	Oct 16, 2022 (156)
54	EVA	ss5391001360	Oct 16, 2022 (156)
55	HUGCELL_USP	ss5478407158	Oct 16, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5575832259	Oct 16, 2022 (156)
57	SANFORD_IMAGENETICS	ss5648485392	Oct 16, 2022 (156)
58	TOMMO_GENOMICS	ss5740559348	Oct 16, 2022 (156)
59	YY_MCH	ss5811106944	Oct 16, 2022 (156)
60	EVA	ss5829909448	Oct 16, 2022 (156)
61	EVA	ss5856981083	Oct 16, 2022 (156)
62	EVA	ss5918487387	Oct 16, 2022 (156)
63	EVA	ss5977699805	Oct 16, 2022 (156)
64	1000Genomes	NC_000009.11 - 141006656	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000009.12 - 138112204	Oct 16, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 141006656	Oct 12, 2018 (152)
67	Genetic variation in the Estonian population	NC_000009.11 - 141006656	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000009.11 - 141006656	Apr 26, 2020 (154)
69	gnomAD - Genomes	NC_000009.12 - 138112204	Apr 26, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000009.11 - 141006656	Apr 26, 2020 (154)
71	KOREAN population from KRGDB	NC_000009.11 - 141006656	Apr 26, 2020 (154)
72	Korean Genome Project	NC_000009.12 - 138112204	Apr 26, 2020 (154)
73	Medical Genome Project healthy controls from Spanish population	NC_000009.11 - 141006656	Apr 26, 2020 (154)
74	Northern Sweden	NC_000009.11 - 141006656	Jul 13, 2019 (153)
75	Qatari	NC_000009.11 - 141006656	Apr 26, 2020 (154)
76	SGDP_PRJ	NC_000009.11 - 141006656	Apr 26, 2020 (154)
77	Siberian	NC_000009.11 - 141006656	Apr 26, 2020 (154)
78	8.3KJPN	NC_000009.11 - 141006656	Apr 26, 2021 (155)
79	14KJPN	NC_000009.12 - 138112204	Oct 16, 2022 (156)
80	TopMed	NC_000009.12 - 138112204	Apr 26, 2021 (155)
81	UK 10K study - Twins	NC_000009.11 - 141006656	Oct 12, 2018 (152)
82	ALFA	NC_000009.12 - 138112204	Apr 26, 2021 (155)
83	ClinVar	RCV001616951.3	Oct 16, 2022 (156)

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
ss109145497, ss280439369, ss485752096, ss1596743554	NC_000009.10:140126476:G:A	NC_000009.12:138112203:G:A	(self)
48241738, 26805509, 19052846, 9465654, 11952998, 28422305, 360733, 10258111, 12454839, 25338393, 6685165, 53808296, 26805509, ss224511991, ss235011911, ss241753010, ss484100932, ss536291177, ss561707608, ss656206435, ss780526750, ss782495603, ss836018284, ss987095642, ss1076687156, ss1335908209, ss1583300717, ss1623796908, ss1666790941, ss1711244973, ss1930412909, ss2025929012, ss2154168811, ss2627432384, ss2634932422, ss2710054661, ss2884496885, ss2986125308, ss3005778895, ss3348910179, ss3630385024, ss3632820120, ss3642719826, ss3673314598, ss3736973246, ss3769833965, ss3831916395, ss3839486873, ss3873321413, ss3921244911, ss5195838989, ss5315442422, ss5391001360, ss5648485392, ss5829909448, ss5977699805	NC_000009.11:141006655:G:A	NC_000009.12:138112203:G:A	(self)
RCV001616951.3, 63358194, 340895807, 23396009, 74396452, 676868513, 12036050096, ss2315370690, ss3026746583, ss3724986572, ss3812991916, ss3844952318, ss3967018008, ss4839490952, ss5282589424, ss5478407158, ss5575832259, ss5740559348, ss5811106944, ss5856981083, ss5918487387	NC_000009.12:138112203:G:A	NC_000009.12:138112203:G:A	(self)
ss104662903, ss158075411	NT_024000.16:1789658:G:A	NC_000009.12:138112203: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 rs72770908

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

rs72770908