Name: rs80274943
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.

rs80274943

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:123630739 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.003752 (993/264690, TOPMED)
A=0.001904 (267/140220, GnomAD)
A=0.00064 (21/32704, ALFA) (+ 13 more)
A=0.05740 (1622/28258, 14KJPN)
A=0.05645 (946/16758, 8.3KJPN)
A=0.0126 (81/6404, 1000G_30x)
A=0.0132 (66/5008, 1000G)
A=0.0002 (1/4480, Estonian)
A=0.0003 (1/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0853 (250/2930, KOREAN)
A=0.0906 (166/1832, Korea1K)
A=0.047 (10/212, Vietnamese)
A=0.03 (1/40, GENOME_DK)
C=0.50 (16/32, SGDP_PRJ)
A=0.50 (16/32, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SCN3B : 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	32704	C=0.99936	A=0.00064
European	Sub	24606	C=0.99976	A=0.00024
African	Sub	5770	C=0.9995	A=0.0005
African Others	Sub	208	C=1.000	A=0.000
African American	Sub	5562	C=0.9995	A=0.0005
Asian	Sub	126	C=0.921	A=0.079
East Asian	Sub	98	C=0.92	A=0.08
Other Asian	Sub	28	C=0.93	A=0.07
Latin American 1	Sub	164	C=1.000	A=0.000
Latin American 2	Sub	684	C=1.000	A=0.000
South Asian	Sub	114	C=0.991	A=0.009
Other	Sub	1240	C=0.9992	A=0.0008

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	C=0.996248	A=0.003752
gnomAD - Genomes	Global	Study-wide	140220	C=0.998096	A=0.001904
gnomAD - Genomes	European	Sub	75942	C=0.99986	A=0.00014
gnomAD - Genomes	African	Sub	42018	C=0.99976	A=0.00024
gnomAD - Genomes	American	Sub	13656	C=0.99993	A=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9994	A=0.0006
gnomAD - Genomes	East Asian	Sub	3126	C=0.9251	A=0.0749
gnomAD - Genomes	Other	Sub	2154	C=0.9958	A=0.0042
Allele Frequency Aggregator	Total	Global	32704	C=0.99936	A=0.00064
Allele Frequency Aggregator	European	Sub	24606	C=0.99976	A=0.00024
Allele Frequency Aggregator	African	Sub	5770	C=0.9995	A=0.0005
Allele Frequency Aggregator	Other	Sub	1240	C=0.9992	A=0.0008
Allele Frequency Aggregator	Latin American 2	Sub	684	C=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	164	C=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	126	C=0.921	A=0.079
Allele Frequency Aggregator	South Asian	Sub	114	C=0.991	A=0.009
14KJPN	JAPANESE	Study-wide	28258	C=0.94260	A=0.05740
8.3KJPN	JAPANESE	Study-wide	16758	C=0.94355	A=0.05645
1000Genomes_30x	Global	Study-wide	6404	C=0.9874	A=0.0126
1000Genomes_30x	African	Sub	1786	C=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	C=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=0.9983	A=0.0017
1000Genomes_30x	East Asian	Sub	1170	C=0.9325	A=0.0675
1000Genomes_30x	American	Sub	980	C=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	C=0.9868	A=0.0132
1000Genomes	African	Sub	1322	C=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9365	A=0.0635
1000Genomes	Europe	Sub	1006	C=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	C=0.998	A=0.002
1000Genomes	American	Sub	694	C=1.000	A=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9998	A=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9997	A=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=1.0000	A=0.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9147	A=0.0853
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9094	A=0.0906
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.953	A=0.047
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	A=0.03
SGDP_PRJ	Global	Study-wide	32	C=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 11	NC_000011.10:g.123630739C>A
GRCh37.p13 chr 11	NC_000011.9:g.123501447C>A
SCN3B RefSeqGene (LRG_421)	NG_016283.1:g.28869G>T

Gene: SCN3B, sodium voltage-gated channel beta subunit 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCN3B transcript variant 1	NM_018400.4:c.*3060=	N/A	3 Prime UTR Variant
SCN3B transcript variant 2	NM_001040151.2:c.*3060=	N/A	3 Prime UTR Variant
SCN3B transcript variant X1	XM_011542897.3:c.23-1289… XM_011542897.3:c.23-1289G>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	C=	A
GRCh38.p14 chr 11	NC_000011.10:g.123630739=	NC_000011.10:g.123630739C>A
GRCh37.p13 chr 11	NC_000011.9:g.123501447=	NC_000011.9:g.123501447C>A
SCN3B RefSeqGene (LRG_421)	NG_016283.1:g.28869=	NG_016283.1:g.28869G>T
SCN3B transcript variant 1	NM_018400.4:c.*3060=	NM_018400.4:c.*3060G>T
SCN3B transcript variant 1	NM_018400.3:c.*3060=	NM_018400.3:c.*3060G>T
SCN3B transcript variant 2	NM_001040151.2:c.*3060=	NM_001040151.2:c.*3060G>T
SCN3B transcript variant 2	NM_001040151.1:c.*3060=	NM_001040151.1:c.*3060G>T
SCN3B transcript variant X1	XM_005271609.1:c.*23-1289=	XM_005271609.1:c.*23-1289G>T
SCN3B transcript variant X1	XM_011542897.3:c.*23-1289=	XM_011542897.3:c.*23-1289G>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#.

38 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss242345967	Jul 15, 2010 (132)
2	ILLUMINA	ss480228204	May 04, 2012 (137)
3	ILLUMINA	ss482748694	May 04, 2012 (137)
4	ILLUMINA	ss533619675	Sep 08, 2015 (146)
5	SSMP	ss658406526	Apr 25, 2013 (138)
6	ILLUMINA	ss779184716	Sep 08, 2015 (146)
7	ILLUMINA	ss781178852	Sep 08, 2015 (146)
8	ILLUMINA	ss834650131	Sep 08, 2015 (146)
9	JMKIDD_LAB	ss1078114149	Aug 21, 2014 (142)
10	1000GENOMES	ss1343319925	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1576006286	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1627655698	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1670649731	Apr 01, 2015 (144)
14	HUMAN_LONGEVITY	ss2186438747	Dec 20, 2016 (150)
15	ILLUMINA	ss2632899791	Nov 08, 2017 (151)
16	GRF	ss2699582635	Nov 08, 2017 (151)
17	GNOMAD	ss2905446779	Nov 08, 2017 (151)
18	AFFY	ss2985602854	Nov 08, 2017 (151)
19	ILLUMINA	ss3626771628	Oct 12, 2018 (152)
20	ILLUMINA	ss3630912892	Oct 12, 2018 (152)
21	EGCUT_WGS	ss3676251725	Jul 13, 2019 (153)
22	EVA	ss3749923315	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3815248270	Jul 13, 2019 (153)
24	SGDP_PRJ	ss3877320719	Apr 26, 2020 (154)
25	KRGDB	ss3925795907	Apr 26, 2020 (154)
26	KOGIC	ss3970934002	Apr 26, 2020 (154)
27	TOPMED	ss4903007964	Apr 26, 2021 (155)
28	TOMMO_GENOMICS	ss5204289036	Apr 26, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5289209128	Oct 16, 2022 (156)
30	EVA	ss5315584364	Oct 16, 2022 (156)
31	EVA	ss5402816212	Oct 16, 2022 (156)
32	HUGCELL_USP	ss5484167681	Oct 16, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5585844458	Oct 16, 2022 (156)
34	SANFORD_IMAGENETICS	ss5652246412	Oct 16, 2022 (156)
35	TOMMO_GENOMICS	ss5752855151	Oct 16, 2022 (156)
36	YY_MCH	ss5812853797	Oct 16, 2022 (156)
37	EVA	ss5922017216	Oct 16, 2022 (156)
38	EVA	ss5943584937	Oct 16, 2022 (156)
39	1000Genomes	NC_000011.9 - 123501447	Oct 12, 2018 (152)
40	1000Genomes_30x	NC_000011.10 - 123630739	Oct 16, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 123501447	Oct 12, 2018 (152)
42	Genetic variation in the Estonian population	NC_000011.9 - 123501447	Oct 12, 2018 (152)
43	The Danish reference pan genome	NC_000011.9 - 123501447	Apr 26, 2020 (154)
44	gnomAD - Genomes	NC_000011.10 - 123630739	Apr 26, 2021 (155)
45	KOREAN population from KRGDB	NC_000011.9 - 123501447	Apr 26, 2020 (154)
46	Korean Genome Project	NC_000011.10 - 123630739	Apr 26, 2020 (154)
47	SGDP_PRJ	NC_000011.9 - 123501447	Apr 26, 2020 (154)
48	8.3KJPN	NC_000011.9 - 123501447	Apr 26, 2021 (155)
49	14KJPN	NC_000011.10 - 123630739	Oct 16, 2022 (156)
50	TopMed	NC_000011.10 - 123630739	Apr 26, 2021 (155)
51	UK 10K study - Twins	NC_000011.9 - 123501447	Oct 12, 2018 (152)
52	A Vietnamese Genetic Variation Database	NC_000011.9 - 123501447	Jul 13, 2019 (153)
53	ALFA	NC_000011.10 - 123630739	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss482748694	NC_000011.8:123006656:C:A	NC_000011.10:123630738:C:A	(self)
55914665, 31043874, 21989973, 2771228, 32973301, 29337699, 62258343, 31043874, 6887626, ss242345967, ss480228204, ss533619675, ss658406526, ss779184716, ss781178852, ss834650131, ss1078114149, ss1343319925, ss1576006286, ss1627655698, ss1670649731, ss2632899791, ss2699582635, ss2905446779, ss2985602854, ss3626771628, ss3630912892, ss3676251725, ss3749923315, ss3877320719, ss3925795907, ss5204289036, ss5315584364, ss5402816212, ss5652246412, ss5943584937	NC_000011.9:123501446:C:A	NC_000011.10:123630738:C:A	(self)
73370393, 394491611, 27312003, 86692255, 118553620, 3853014354, ss2186438747, ss3815248270, ss3970934002, ss4903007964, ss5289209128, ss5484167681, ss5585844458, ss5752855151, ss5812853797, ss5922017216	NC_000011.10:123630738:C:A	NC_000011.10:123630738:C: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 rs80274943

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

rs80274943