Name: rs7976351
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.

rs7976351

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:51767630 (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: A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.086445 (22881/264690, TOPMED)
T=0.081101 (11371/140208, GnomAD)
T=0.04947 (1398/28258, 14KJPN) (+ 16 more)
T=0.05903 (1115/18890, ALFA)
T=0.04887 (819/16760, 8.3KJPN)
T=0.1112 (712/6404, 1000G_30x)
T=0.1068 (535/5008, 1000G)
T=0.0223 (100/4480, Estonian)
T=0.0340 (131/3854, ALSPAC)
T=0.0275 (102/3708, TWINSUK)
T=0.0689 (202/2930, KOREAN)
T=0.1351 (255/1888, HapMap)
T=0.017 (17/998, GoNL)
T=0.032 (19/600, NorthernSweden)
T=0.102 (22/216, Qatari)
T=0.042 (9/216, Vietnamese)
A=0.413 (57/138, SGDP_PRJ)
A=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SCN8A : 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	A=0.94097	T=0.05903
European	Sub	14286	A=0.97284	T=0.02716
African	Sub	2946	A=0.7895	T=0.2105
African Others	Sub	114	A=0.711	T=0.289
African American	Sub	2832	A=0.7927	T=0.2073
Asian	Sub	112	A=0.955	T=0.045
East Asian	Sub	86	A=0.95	T=0.05
Other Asian	Sub	26	A=0.96	T=0.04
Latin American 1	Sub	146	A=0.890	T=0.110
Latin American 2	Sub	610	A=0.954	T=0.046
South Asian	Sub	98	A=0.91	T=0.09
Other	Sub	692	A=0.929	T=0.071

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	A=0.913555	T=0.086445
gnomAD - Genomes	Global	Study-wide	140208	A=0.918899	T=0.081101
gnomAD - Genomes	European	Sub	75954	A=0.97265	T=0.02735
gnomAD - Genomes	African	Sub	41984	A=0.80259	T=0.19741
gnomAD - Genomes	American	Sub	13660	A=0.95871	T=0.04129
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9789	T=0.0211
gnomAD - Genomes	East Asian	Sub	3134	A=0.9320	T=0.0680
gnomAD - Genomes	Other	Sub	2152	A=0.9261	T=0.0739
14KJPN	JAPANESE	Study-wide	28258	A=0.95053	T=0.04947
Allele Frequency Aggregator	Total	Global	18890	A=0.94097	T=0.05903
Allele Frequency Aggregator	European	Sub	14286	A=0.97284	T=0.02716
Allele Frequency Aggregator	African	Sub	2946	A=0.7895	T=0.2105
Allele Frequency Aggregator	Other	Sub	692	A=0.929	T=0.071
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.954	T=0.046
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.890	T=0.110
Allele Frequency Aggregator	Asian	Sub	112	A=0.955	T=0.045
Allele Frequency Aggregator	South Asian	Sub	98	A=0.91	T=0.09
8.3KJPN	JAPANESE	Study-wide	16760	A=0.95113	T=0.04887
1000Genomes_30x	Global	Study-wide	6404	A=0.8888	T=0.1112
1000Genomes_30x	African	Sub	1786	A=0.7744	T=0.2256
1000Genomes_30x	Europe	Sub	1266	A=0.9621	T=0.0379
1000Genomes_30x	South Asian	Sub	1202	A=0.8844	T=0.1156
1000Genomes_30x	East Asian	Sub	1170	A=0.9274	T=0.0726
1000Genomes_30x	American	Sub	980	A=0.962	T=0.038
1000Genomes	Global	Study-wide	5008	A=0.8932	T=0.1068
1000Genomes	African	Sub	1322	A=0.7799	T=0.2201
1000Genomes	East Asian	Sub	1008	A=0.9286	T=0.0714
1000Genomes	Europe	Sub	1006	A=0.9632	T=0.0368
1000Genomes	South Asian	Sub	978	A=0.891	T=0.109
1000Genomes	American	Sub	694	A=0.960	T=0.040
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9777	T=0.0223
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9660	T=0.0340
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9725	T=0.0275
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9311	T=0.0689
HapMap	Global	Study-wide	1888	A=0.8649	T=0.1351
HapMap	American	Sub	770	A=0.929	T=0.071
HapMap	African	Sub	690	A=0.746	T=0.254
HapMap	Asian	Sub	254	A=0.937	T=0.063
HapMap	Europe	Sub	174	A=0.948	T=0.052
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.983	T=0.017
Northern Sweden	ACPOP	Study-wide	600	A=0.968	T=0.032
Qatari	Global	Study-wide	216	A=0.898	T=0.102
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.958	T=0.042
SGDP_PRJ	Global	Study-wide	138	A=0.413	T=0.587
Siberian	Global	Study-wide	4	A=0.5	T=0.5

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.51767630A>T
GRCh37.p13 chr 12	NC_000012.11:g.52161414A>T
SCN8A RefSeqGene (LRG_1389)	NG_021180.3:g.182673A>T

Gene: SCN8A, sodium voltage-gated channel alpha subunit 8 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCN8A transcript variant 2	NM_001177984.3:c.2902-123… NM_001177984.3:c.2902-1235A>T	N/A	Intron Variant
SCN8A transcript variant 3	NM_001330260.2:c.2902-123… NM_001330260.2:c.2902-1235A>T	N/A	Intron Variant
SCN8A transcript variant 4	NM_001369788.1:c.2902-123… NM_001369788.1:c.2902-1235A>T	N/A	Intron Variant
SCN8A transcript variant 1	NM_014191.4:c.2902-1235A>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	A=	T
GRCh38.p14 chr 12	NC_000012.12:g.51767630=	NC_000012.12:g.51767630A>T
GRCh37.p13 chr 12	NC_000012.11:g.52161414=	NC_000012.11:g.52161414A>T
SCN8A RefSeqGene (LRG_1389)	NG_021180.3:g.182673=	NG_021180.3:g.182673A>T
SCN8A transcript variant 2	NM_001177984.2:c.2902-1235=	NM_001177984.2:c.2902-1235A>T
SCN8A transcript variant 2	NM_001177984.3:c.2902-1235=	NM_001177984.3:c.2902-1235A>T
SCN8A transcript variant 3	NM_001330260.2:c.2902-1235=	NM_001330260.2:c.2902-1235A>T
SCN8A transcript variant 4	NM_001369788.1:c.2902-1235=	NM_001369788.1:c.2902-1235A>T
SCN8A transcript variant 1	NM_014191.3:c.2902-1235=	NM_014191.3:c.2902-1235A>T
SCN8A transcript variant 1	NM_014191.4:c.2902-1235=	NM_014191.4:c.2902-1235A>T
SCN8A transcript variant X1	XM_005269075.1:c.2935-1235=	XM_005269075.1:c.2935-1235A>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#.

57 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss12219150	Jul 11, 2003 (116)
2	PERLEGEN	ss23407341	Sep 20, 2004 (123)
3	AFFY	ss66365057	Nov 29, 2006 (127)
4	AFFY	ss76086785	Dec 06, 2007 (129)
5	KRIBB_YJKIM	ss82526905	Dec 15, 2007 (130)
6	BGI	ss103048098	Dec 01, 2009 (131)
7	ILLUMINA-UK	ss118804179	Feb 14, 2009 (130)
8	GMI	ss157472827	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss169834173	Jul 04, 2010 (132)
10	AFFY	ss172455965	Jul 04, 2010 (132)
11	BUSHMAN	ss198176389	Jul 04, 2010 (132)
12	1000GENOMES	ss211282955	Jul 14, 2010 (132)
13	1000GENOMES	ss225752764	Jul 14, 2010 (132)
14	1000GENOMES	ss242494228	Jul 15, 2010 (132)
15	GMI	ss281396561	May 04, 2012 (137)
16	TISHKOFF	ss563165835	Apr 25, 2013 (138)
17	SSMP	ss658721454	Apr 25, 2013 (138)
18	EVA-GONL	ss989533738	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1078460845	Aug 21, 2014 (142)
20	1000GENOMES	ss1345016654	Aug 21, 2014 (142)
21	DDI	ss1426933052	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1628591607	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1671585640	Apr 01, 2015 (144)
24	EVA_SVP	ss1713327530	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1807245351	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1932897921	Feb 12, 2016 (147)
27	JJLAB	ss2027199894	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2155537699	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2189792338	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2628080692	Nov 08, 2017 (151)
31	GRF	ss2699881251	Nov 08, 2017 (151)
32	GNOMAD	ss2910508280	Nov 08, 2017 (151)
33	AFFY	ss2985616751	Nov 08, 2017 (151)
34	SWEGEN	ss3009688809	Nov 08, 2017 (151)
35	EGCUT_WGS	ss3676961428	Jul 13, 2019 (153)
36	EVA_DECODE	ss3693671673	Jul 13, 2019 (153)
37	ACPOP	ss3739022200	Jul 13, 2019 (153)
38	EVA	ss3750480197	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3815809482	Jul 13, 2019 (153)
40	EVA	ss3833122996	Apr 27, 2020 (154)
41	EVA	ss3840131620	Apr 27, 2020 (154)
42	EVA	ss3845618045	Apr 27, 2020 (154)
43	SGDP_PRJ	ss3878274187	Apr 27, 2020 (154)
44	KRGDB	ss3926906586	Apr 27, 2020 (154)
45	TOPMED	ss4918308588	Apr 26, 2021 (155)
46	TOMMO_GENOMICS	ss5206324086	Apr 26, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5290810791	Oct 16, 2022 (156)
48	EVA	ss5405638406	Oct 16, 2022 (156)
49	HUGCELL_USP	ss5485564136	Oct 16, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5588297973	Oct 16, 2022 (156)
51	SANFORD_IMAGENETICS	ss5653153671	Oct 16, 2022 (156)
52	TOMMO_GENOMICS	ss5756116327	Oct 16, 2022 (156)
53	YY_MCH	ss5813298843	Oct 16, 2022 (156)
54	EVA	ss5837966704	Oct 16, 2022 (156)
55	EVA	ss5850381414	Oct 16, 2022 (156)
56	EVA	ss5904394111	Oct 16, 2022 (156)
57	EVA	ss5944517119	Oct 16, 2022 (156)
58	1000Genomes	NC_000012.11 - 52161414	Oct 12, 2018 (152)
59	1000Genomes_30x	NC_000012.12 - 51767630	Oct 16, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 52161414	Oct 12, 2018 (152)
61	Genetic variation in the Estonian population	NC_000012.11 - 52161414	Oct 12, 2018 (152)
62	gnomAD - Genomes	NC_000012.12 - 51767630	Apr 26, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000012.11 - 52161414	Apr 27, 2020 (154)
64	HapMap	NC_000012.12 - 51767630	Apr 27, 2020 (154)
65	KOREAN population from KRGDB	NC_000012.11 - 52161414	Apr 27, 2020 (154)
66	Northern Sweden	NC_000012.11 - 52161414	Jul 13, 2019 (153)
67	Qatari	NC_000012.11 - 52161414	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000012.11 - 52161414	Apr 27, 2020 (154)
69	Siberian	NC_000012.11 - 52161414	Apr 27, 2020 (154)
70	8.3KJPN	NC_000012.11 - 52161414	Apr 26, 2021 (155)
71	14KJPN	NC_000012.12 - 51767630	Oct 16, 2022 (156)
72	TopMed	NC_000012.12 - 51767630	Apr 26, 2021 (155)
73	UK 10K study - Twins	NC_000012.11 - 52161414	Oct 12, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000012.11 - 52161414	Jul 13, 2019 (153)
75	ALFA	NC_000012.12 - 51767630	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)
rs59652974	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66365057, ss76086785, ss118804179, ss169834173, ss172455965, ss198176389, ss211282955, ss281396561, ss1713327530	NC_000012.10:50447680:A:T	NC_000012.12:51767629:A:T	(self)
57765771, 32076099, 22699676, 14313760, 34083980, 12307065, 14939851, 30291167, 8054053, 64293393, 32076099, 7120727, ss225752764, ss242494228, ss563165835, ss658721454, ss989533738, ss1078460845, ss1345016654, ss1426933052, ss1628591607, ss1671585640, ss1807245351, ss1932897921, ss2027199894, ss2155537699, ss2628080692, ss2699881251, ss2910508280, ss2985616751, ss3009688809, ss3676961428, ss3739022200, ss3750480197, ss3833122996, ss3840131620, ss3878274187, ss3926906586, ss5206324086, ss5405638406, ss5653153671, ss5837966704, ss5944517119	NC_000012.11:52161413:A:T	NC_000012.12:51767629:A:T	(self)
75823908, 407355978, 816080, 89953431, 133854245, 9826171243, ss2189792338, ss3693671673, ss3815809482, ss3845618045, ss4918308588, ss5290810791, ss5485564136, ss5588297973, ss5756116327, ss5813298843, ss5850381414, ss5904394111	NC_000012.12:51767629:A:T	NC_000012.12:51767629:A:T	(self)
ss12219150	NT_029419.10:14304719:A:T	NC_000012.12:51767629:A:T	(self)
ss23407341, ss82526905, ss103048098, ss157472827	NT_029419.12:14304719:A:T	NC_000012.12:51767629:A:T	(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 rs7976351

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

rs7976351