Name: rs17125933
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.

rs17125933

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:51635889 (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=0.064649 (17112/264690, TOPMED)
T=0.058354 (8182/140214, GnomAD)
T=0.14863 (4200/28258, 14KJPN) (+ 17 more)
T=0.04341 (820/18890, ALFA)
T=0.14654 (2456/16760, 8.3KJPN)
T=0.0957 (613/6404, 1000G_30x)
T=0.0950 (476/5008, 1000G)
T=0.0228 (102/4480, Estonian)
T=0.0324 (125/3854, ALSPAC)
T=0.0294 (109/3708, TWINSUK)
T=0.1642 (481/2930, KOREAN)
T=0.1648 (302/1832, Korea1K)
T=0.017 (17/998, GoNL)
T=0.032 (19/600, NorthernSweden)
T=0.088 (19/216, Qatari)
T=0.089 (19/214, Vietnamese)
T=0.090 (19/210, HapMap)
A=0.434 (59/136, 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=0.95659	T=0.04341
European	Sub	14286	A=0.97354	T=0.02646
African	Sub	2946	A=0.8846	T=0.1154
African Others	Sub	114	A=0.895	T=0.105
African American	Sub	2832	A=0.8842	T=0.1158
Asian	Sub	112	A=0.893	T=0.107
East Asian	Sub	86	A=0.88	T=0.12
Other Asian	Sub	26	A=0.92	T=0.08
Latin American 1	Sub	146	A=0.945	T=0.055
Latin American 2	Sub	610	A=0.951	T=0.049
South Asian	Sub	98	A=0.89	T=0.11
Other	Sub	692	A=0.941	T=0.059

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=0.935351	T=0.064649
gnomAD - Genomes	Global	Study-wide	140214	A=0.941646	T=0.058354
gnomAD - Genomes	European	Sub	75928	A=0.97316	T=0.02684
gnomAD - Genomes	African	Sub	42010	A=0.88788	T=0.11212
gnomAD - Genomes	American	Sub	13670	A=0.95128	T=0.04872
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.9365	T=0.0635
gnomAD - Genomes	East Asian	Sub	3130	A=0.8652	T=0.1348
gnomAD - Genomes	Other	Sub	2154	A=0.9373	T=0.0627
14KJPN	JAPANESE	Study-wide	28258	A=0.85137	T=0.14863
Allele Frequency Aggregator	Total	Global	18890	A=0.95659	T=0.04341
Allele Frequency Aggregator	European	Sub	14286	A=0.97354	T=0.02646
Allele Frequency Aggregator	African	Sub	2946	A=0.8846	T=0.1154
Allele Frequency Aggregator	Other	Sub	692	A=0.941	T=0.059
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.951	T=0.049
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.945	T=0.055
Allele Frequency Aggregator	Asian	Sub	112	A=0.893	T=0.107
Allele Frequency Aggregator	South Asian	Sub	98	A=0.89	T=0.11
8.3KJPN	JAPANESE	Study-wide	16760	A=0.85346	T=0.14654
1000Genomes_30x	Global	Study-wide	6404	A=0.9043	T=0.0957
1000Genomes_30x	African	Sub	1786	A=0.8667	T=0.1333
1000Genomes_30x	Europe	Sub	1266	A=0.9597	T=0.0403
1000Genomes_30x	South Asian	Sub	1202	A=0.8977	T=0.1023
1000Genomes_30x	East Asian	Sub	1170	A=0.8709	T=0.1291
1000Genomes_30x	American	Sub	980	A=0.949	T=0.051
1000Genomes	Global	Study-wide	5008	A=0.9050	T=0.0950
1000Genomes	African	Sub	1322	A=0.8691	T=0.1309
1000Genomes	East Asian	Sub	1008	A=0.8700	T=0.1300
1000Genomes	Europe	Sub	1006	A=0.9612	T=0.0388
1000Genomes	South Asian	Sub	978	A=0.903	T=0.097
1000Genomes	American	Sub	694	A=0.945	T=0.055
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9772	T=0.0228
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9676	T=0.0324
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9706	T=0.0294
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.8358	T=0.1642
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8352	T=0.1648
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=0.912	T=0.088
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.911	T=0.089
HapMap	Global	Study-wide	210	A=0.910	T=0.090
HapMap	American	Sub	120	A=0.975	T=0.025
HapMap	Asian	Sub	90	A=0.82	T=0.18
SGDP_PRJ	Global	Study-wide	136	A=0.434	T=0.566
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.51635889A>T
GRCh37.p13 chr 12	NC_000012.11:g.52029673A>T
SCN8A RefSeqGene (LRG_1389)	NG_021180.3:g.50932A>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.-54-2687… NM_001177984.3:c.-54-26875A>T	N/A	Intron Variant
SCN8A transcript variant 3	NM_001330260.2:c.-54-2687… NM_001330260.2:c.-54-26875A>T	N/A	Intron Variant
SCN8A transcript variant 4	NM_001369788.1:c.-54-2687… NM_001369788.1:c.-54-26875A>T	N/A	Intron Variant
SCN8A transcript variant 1	NM_014191.4:c.-54-26875A>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.51635889=	NC_000012.12:g.51635889A>T
GRCh37.p13 chr 12	NC_000012.11:g.52029673=	NC_000012.11:g.52029673A>T
SCN8A RefSeqGene (LRG_1389)	NG_021180.3:g.50932=	NG_021180.3:g.50932A>T
SCN8A transcript variant 2	NM_001177984.2:c.-54-26875=	NM_001177984.2:c.-54-26875A>T
SCN8A transcript variant 2	NM_001177984.3:c.-54-26875=	NM_001177984.3:c.-54-26875A>T
SCN8A transcript variant 3	NM_001330260.2:c.-54-26875=	NM_001330260.2:c.-54-26875A>T
SCN8A transcript variant 4	NM_001369788.1:c.-54-26875=	NM_001369788.1:c.-54-26875A>T
SCN8A transcript variant 1	NM_014191.3:c.-54-26875=	NM_014191.3:c.-54-26875A>T
SCN8A transcript variant 1	NM_014191.4:c.-54-26875=	NM_014191.4:c.-54-26875A>T
SCN8A transcript variant X1	XM_005269075.1:c.-54-26875=	XM_005269075.1:c.-54-26875A>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#.

56 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss23407094	Sep 20, 2004 (123)
2	HGSV	ss80732044	Dec 15, 2007 (130)
3	HGSV	ss83915599	Dec 15, 2007 (130)
4	KRIBB_YJKIM	ss104806480	Feb 05, 2009 (130)
5	BGI	ss106806095	Feb 05, 2009 (130)
6	ILLUMINA-UK	ss118803577	Feb 14, 2009 (130)
7	GMI	ss157471901	Dec 01, 2009 (131)
8	BUSHMAN	ss198175549	Jul 04, 2010 (132)
9	1000GENOMES	ss225752463	Jul 14, 2010 (132)
10	1000GENOMES	ss242494058	Jul 15, 2010 (132)
11	GMI	ss281396324	May 04, 2012 (137)
12	SSMP	ss658720986	Apr 25, 2013 (138)
13	EVA-GONL	ss989533012	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1078460444	Aug 21, 2014 (142)
15	1000GENOMES	ss1345013647	Aug 21, 2014 (142)
16	EVA_DECODE	ss1599204465	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1628590043	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1671584076	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1807245094	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1932897216	Feb 12, 2016 (147)
21	GENOMED	ss1967589658	Jul 19, 2016 (147)
22	JJLAB	ss2027199572	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2155537401	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2189785903	Dec 20, 2016 (150)
25	SYSTEMSBIOZJU	ss2628080509	Nov 08, 2017 (151)
26	GRF	ss2699880905	Nov 08, 2017 (151)
27	GNOMAD	ss2910498901	Nov 08, 2017 (151)
28	SWEGEN	ss3009687584	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3645252956	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3676960234	Jul 13, 2019 (153)
31	EVA_DECODE	ss3693670261	Jul 13, 2019 (153)
32	ACPOP	ss3739021662	Jul 13, 2019 (153)
33	EVA	ss3750479316	Jul 13, 2019 (153)
34	PACBIO	ss3787226572	Jul 13, 2019 (153)
35	PACBIO	ss3792328249	Jul 13, 2019 (153)
36	PACBIO	ss3797211034	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3815808625	Jul 13, 2019 (153)
38	EVA	ss3833122745	Apr 27, 2020 (154)
39	EVA	ss3840131427	Apr 27, 2020 (154)
40	EVA	ss3845617852	Apr 27, 2020 (154)
41	SGDP_PRJ	ss3878272786	Apr 27, 2020 (154)
42	KRGDB	ss3926904807	Apr 27, 2020 (154)
43	KOGIC	ss3971932534	Apr 27, 2020 (154)
44	TOPMED	ss4918279655	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5206320568	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5290808180	Oct 16, 2022 (156)
47	EVA	ss5405633462	Oct 16, 2022 (156)
48	HUGCELL_USP	ss5485561842	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5588294002	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5653152312	Oct 16, 2022 (156)
51	TOMMO_GENOMICS	ss5756111724	Oct 16, 2022 (156)
52	YY_MCH	ss5813298269	Oct 16, 2022 (156)
53	EVA	ss5837965809	Oct 16, 2022 (156)
54	EVA	ss5850381185	Oct 16, 2022 (156)
55	EVA	ss5904391098	Oct 16, 2022 (156)
56	EVA	ss5944515694	Oct 16, 2022 (156)
57	1000Genomes	NC_000012.11 - 52029673	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000012.12 - 51635889	Oct 16, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 52029673	Oct 12, 2018 (152)
60	Genetic variation in the Estonian population	NC_000012.11 - 52029673	Oct 12, 2018 (152)
61	gnomAD - Genomes	NC_000012.12 - 51635889	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000012.11 - 52029673	Apr 27, 2020 (154)
63	HapMap	NC_000012.12 - 51635889	Apr 27, 2020 (154)
64	KOREAN population from KRGDB	NC_000012.11 - 52029673	Apr 27, 2020 (154)
65	Korean Genome Project	NC_000012.12 - 51635889	Apr 27, 2020 (154)
66	Northern Sweden	NC_000012.11 - 52029673	Jul 13, 2019 (153)
67	Qatari	NC_000012.11 - 52029673	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000012.11 - 52029673	Apr 27, 2020 (154)
69	Siberian	NC_000012.11 - 52029673	Apr 27, 2020 (154)
70	8.3KJPN	NC_000012.11 - 52029673	Apr 26, 2021 (155)
71	14KJPN	NC_000012.12 - 51635889	Oct 16, 2022 (156)
72	TopMed	NC_000012.12 - 51635889	Apr 26, 2021 (155)
73	UK 10K study - Twins	NC_000012.11 - 52029673	Oct 12, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000012.11 - 52029673	Jul 13, 2019 (153)
75	ALFA	NC_000012.12 - 51635889	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)
rs58944935	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80732044, ss83915599	NC_000012.9:50315939:A:T	NC_000012.12:51635888:A:T	(self)
ss118803577, ss198175549, ss281396324, ss1599204465	NC_000012.10:50315939:A:T	NC_000012.12:51635888:A:T	(self)
57762660, 32074393, 22698482, 14313051, 34082201, 12306527, 14939146, 30289766, 8053755, 64289875, 32074393, 7120403, ss225752463, ss242494058, ss658720986, ss989533012, ss1078460444, ss1345013647, ss1628590043, ss1671584076, ss1807245094, ss1932897216, ss1967589658, ss2027199572, ss2155537401, ss2628080509, ss2699880905, ss2910498901, ss3009687584, ss3676960234, ss3739021662, ss3750479316, ss3787226572, ss3792328249, ss3797211034, ss3833122745, ss3840131427, ss3878272786, ss3926904807, ss5206320568, ss5405633462, ss5653152312, ss5837965809, ss5944515694	NC_000012.11:52029672:A:T	NC_000012.12:51635888:A:T	(self)
75819937, 407332375, 815967, 28310535, 89948828, 133825312, 704850937, ss2189785903, ss3645252956, ss3693670261, ss3815808625, ss3845617852, ss3971932534, ss4918279655, ss5290808180, ss5485561842, ss5588294002, ss5756111724, ss5813298269, ss5850381185, ss5904391098	NC_000012.12:51635888:A:T	NC_000012.12:51635888:A:T	(self)
ss23407094, ss104806480, ss106806095, ss157471901	NT_029419.12:14172978:A:T	NC_000012.12:51635888: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 rs17125933

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

rs17125933