Name: rs199473596
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.

rs199473596

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:38575379 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000008 (2/264690, TOPMED)
T=0.000025 (6/241892, GnomAD_exome)
T=0.00005 (4/88516, ExAC) (+ 2 more)
G=0.00000 (0/14050, ALFA)
T=0.00000 (0/14050, ALFA)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SCN5A : Missense Variant
Publications: 2 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	14050	C=1.00000	G=0.00000, T=0.00000
European	Sub	9690	C=1.0000	G=0.0000, T=0.0000
African	Sub	2898	C=1.0000	G=0.0000, T=0.0000
African Others	Sub	114	C=1.000	G=0.000, T=0.000
African American	Sub	2784	C=1.0000	G=0.0000, T=0.0000
Asian	Sub	112	C=1.000	G=0.000, T=0.000
East Asian	Sub	86	C=1.00	G=0.00, T=0.00
Other Asian	Sub	26	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	610	C=1.000	G=0.000, T=0.000
South Asian	Sub	98	C=1.00	G=0.00, T=0.00
Other	Sub	496	C=1.000	G=0.000, T=0.000

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=0.999992	T=0.000008
gnomAD - Exomes	Global	Study-wide	241892	C=0.999975	T=0.000025
gnomAD - Exomes	European	Sub	130068	C=0.999954	T=0.000046
gnomAD - Exomes	Asian	Sub	47254	C=1.00000	T=0.00000
gnomAD - Exomes	American	Sub	33732	C=1.00000	T=0.00000
gnomAD - Exomes	African	Sub	15040	C=1.00000	T=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9860	C=1.0000	T=0.0000
gnomAD - Exomes	Other	Sub	5938	C=1.0000	T=0.0000
ExAC	Global	Study-wide	88516	C=0.99995	T=0.00005
ExAC	Europe	Sub	54014	C=0.99993	T=0.00007
ExAC	Asian	Sub	19128	C=1.00000	T=0.00000
ExAC	American	Sub	7430	C=1.0000	T=0.0000
ExAC	African	Sub	7316	C=1.0000	T=0.0000
ExAC	Other	Sub	628	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	14050	C=1.00000	G=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	9690	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	2898	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	496	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	G=0.00, T=0.00

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 3	NC_000003.12:g.38575379C>G
GRCh38.p14 chr 3	NC_000003.12:g.38575379C>T
GRCh37.p13 chr 3	NC_000003.11:g.38616870C>G
GRCh37.p13 chr 3	NC_000003.11:g.38616870C>T
SCN5A RefSeqGene (LRG_289)	NG_008934.1:g.79294G>C
SCN5A RefSeqGene (LRG_289)	NG_008934.1:g.79294G>A

Gene: SCN5A, sodium voltage-gated channel alpha subunit 5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCN5A transcript variant 7	NM_001354701.2:c.3581G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform g	NP_001341630.1:p.Arg1194P… NP_001341630.1:p.Arg1194Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 7	NM_001354701.2:c.3581G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform g	NP_001341630.1:p.Arg1194H… NP_001341630.1:p.Arg1194His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant 5	NM_001160160.2:c.3581G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform e	NP_001153632.1:p.Arg1194P… NP_001153632.1:p.Arg1194Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 5	NM_001160160.2:c.3581G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform e	NP_001153632.1:p.Arg1194H… NP_001153632.1:p.Arg1194His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant 2	NM_000335.5:c.3581G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform b	NP_000326.2:p.Arg1194Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 2	NM_000335.5:c.3581G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform b	NP_000326.2:p.Arg1194His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant 4	NM_001099405.2:c.3584G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform d	NP_001092875.1:p.Arg1195P… NP_001092875.1:p.Arg1195Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 4	NM_001099405.2:c.3584G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform d	NP_001092875.1:p.Arg1195H… NP_001092875.1:p.Arg1195His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant 3	NM_001099404.2:c.3584G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform c	NP_001092874.1:p.Arg1195P… NP_001092874.1:p.Arg1195Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 3	NM_001099404.2:c.3584G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform c	NP_001092874.1:p.Arg1195H… NP_001092874.1:p.Arg1195His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant 6	NM_001160161.2:c.3422G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform f	NP_001153633.1:p.Arg1141P… NP_001153633.1:p.Arg1141Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 6	NM_001160161.2:c.3422G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform f	NP_001153633.1:p.Arg1141H… NP_001153633.1:p.Arg1141His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant 1	NM_198056.3:c.3584G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform a	NP_932173.1:p.Arg1195Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant 1	NM_198056.3:c.3584G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform a	NP_932173.1:p.Arg1195His	R (Arg) > H (His)	Missense Variant
SCN5A transcript variant X1	XM_011533991.3:c.3581G>C	R [CGC] > P [CCC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform X1	XP_011532293.1:p.Arg1194P… XP_011532293.1:p.Arg1194Pro	R (Arg) > P (Pro)	Missense Variant
SCN5A transcript variant X1	XM_011533991.3:c.3581G>A	R [CGC] > H [CAC]	Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform X1	XP_011532293.1:p.Arg1194H… XP_011532293.1:p.Arg1194His	R (Arg) > H (His)	Missense 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: T (allele ID: 78699 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000058579.4	Ventricular tachycardia	Not-Provided
RCV001306977.2	Brugada syndrome	Uncertain-Significance
RCV001842339.2	Cardiac arrhythmia	Uncertain-Significance

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=	G	T
GRCh38.p14 chr 3	NC_000003.12:g.38575379=	NC_000003.12:g.38575379C>G	NC_000003.12:g.38575379C>T
GRCh37.p13 chr 3	NC_000003.11:g.38616870=	NC_000003.11:g.38616870C>G	NC_000003.11:g.38616870C>T
SCN5A RefSeqGene (LRG_289)	NG_008934.1:g.79294=	NG_008934.1:g.79294G>C	NG_008934.1:g.79294G>A
SCN5A transcript variant 2	NM_000335.5:c.3581=	NM_000335.5:c.3581G>C	NM_000335.5:c.3581G>A
SCN5A transcript variant 2	NM_000335.4:c.3581=	NM_000335.4:c.3581G>C	NM_000335.4:c.3581G>A
SCN5A transcript variant 1	NM_198056.3:c.3584=	NM_198056.3:c.3584G>C	NM_198056.3:c.3584G>A
SCN5A transcript variant 1	NM_198056.2:c.3584=	NM_198056.2:c.3584G>C	NM_198056.2:c.3584G>A
SCN5A transcript variant 3	NM_001099404.2:c.3584=	NM_001099404.2:c.3584G>C	NM_001099404.2:c.3584G>A
SCN5A transcript variant 3	NM_001099404.1:c.3584=	NM_001099404.1:c.3584G>C	NM_001099404.1:c.3584G>A
SCN5A transcript variant 4	NM_001099405.2:c.3584=	NM_001099405.2:c.3584G>C	NM_001099405.2:c.3584G>A
SCN5A transcript variant 4	NM_001099405.1:c.3584=	NM_001099405.1:c.3584G>C	NM_001099405.1:c.3584G>A
SCN5A transcript variant 7	NM_001354701.2:c.3581=	NM_001354701.2:c.3581G>C	NM_001354701.2:c.3581G>A
SCN5A transcript variant 7	NM_001354701.1:c.3581=	NM_001354701.1:c.3581G>C	NM_001354701.1:c.3581G>A
SCN5A transcript variant 5	NM_001160160.2:c.3581=	NM_001160160.2:c.3581G>C	NM_001160160.2:c.3581G>A
SCN5A transcript variant 5	NM_001160160.1:c.3581=	NM_001160160.1:c.3581G>C	NM_001160160.1:c.3581G>A
SCN5A transcript variant 6	NM_001160161.2:c.3422=	NM_001160161.2:c.3422G>C	NM_001160161.2:c.3422G>A
SCN5A transcript variant 6	NM_001160161.1:c.3422=	NM_001160161.1:c.3422G>C	NM_001160161.1:c.3422G>A
SCN5A transcript variant 11	NR_176299.1:n.4330=	NR_176299.1:n.4330G>C	NR_176299.1:n.4330G>A
SCN5A transcript variant X1	XM_011533991.3:c.3581=	XM_011533991.3:c.3581G>C	XM_011533991.3:c.3581G>A
SCN5A transcript variant X1	XM_011533991.2:c.3581=	XM_011533991.2:c.3581G>C	XM_011533991.2:c.3581G>A
SCN5A transcript variant X2	XM_011533991.1:c.3581=	XM_011533991.1:c.3581G>C	XM_011533991.1:c.3581G>A
sodium channel protein type 5 subunit alpha isoform b	NP_000326.2:p.Arg1194=	NP_000326.2:p.Arg1194Pro	NP_000326.2:p.Arg1194His
sodium channel protein type 5 subunit alpha isoform a	NP_932173.1:p.Arg1195=	NP_932173.1:p.Arg1195Pro	NP_932173.1:p.Arg1195His
sodium channel protein type 5 subunit alpha isoform c	NP_001092874.1:p.Arg1195=	NP_001092874.1:p.Arg1195Pro	NP_001092874.1:p.Arg1195His
sodium channel protein type 5 subunit alpha isoform d	NP_001092875.1:p.Arg1195=	NP_001092875.1:p.Arg1195Pro	NP_001092875.1:p.Arg1195His
sodium channel protein type 5 subunit alpha isoform g	NP_001341630.1:p.Arg1194=	NP_001341630.1:p.Arg1194Pro	NP_001341630.1:p.Arg1194His
sodium channel protein type 5 subunit alpha isoform e	NP_001153632.1:p.Arg1194=	NP_001153632.1:p.Arg1194Pro	NP_001153632.1:p.Arg1194His
sodium channel protein type 5 subunit alpha isoform f	NP_001153633.1:p.Arg1141=	NP_001153633.1:p.Arg1141Pro	NP_001153633.1:p.Arg1141His
sodium channel protein type 5 subunit alpha isoform X1	XP_011532293.1:p.Arg1194=	XP_011532293.1:p.Arg1194Pro	XP_011532293.1:p.Arg1194His

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#.

4 SubSNP, 4 Frequency, 3 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	RBH_CV_BRU	ss487104519	Feb 13, 2012 (136)
2	EVA_EXAC	ss1686932870	Apr 01, 2015 (144)
3	GNOMAD	ss2733639348	Nov 08, 2017 (151)
4	TOPMED	ss4561188795	Apr 27, 2021 (155)
5	ExAC	NC_000003.11 - 38616870	Oct 12, 2018 (152)
6	gnomAD - Exomes	NC_000003.11 - 38616870	Jul 13, 2019 (153)
7	TopMed	NC_000003.12 - 38575379	Apr 27, 2021 (155)
8	ALFA	NC_000003.12 - 38575379	Apr 27, 2021 (155)
9	ClinVar	RCV000058579.4	Oct 13, 2022 (156)
10	ClinVar	RCV001306977.2	Oct 13, 2022 (156)
11	ClinVar	RCV001842339.2	Oct 13, 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
ss2733639348	NC_000003.11:38616869:C:G	NC_000003.12:38575378:C:G	(self)
5982137892	NC_000003.12:38575378:C:G	NC_000003.12:38575378:C:G	(self)
6852009, 2714245, ss1686932870, ss2733639348	NC_000003.11:38616869:C:T	NC_000003.12:38575378:C:T	(self)
RCV000058579.4, RCV001306977.2, RCV001842339.2, 398566350, 5982137892, ss487104519, ss4561188795	NC_000003.12:38575378:C:T	NC_000003.12:38575378:C:T	(self)

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

2 citations for rs199473596

PMID	Title	Author	Year	Journal
19632629	Unique mixed phenotype and unexpected functional effect revealed by novel compound heterozygosity mutations involving SCN5A.	Medeiros-Domingo A et al.	2009	Heart rhythm
22581653	Paralogous annotation of disease-causing variants in long QT syndrome genes.	Ware JS et al.	2012	Human mutation

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

rs199473596