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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs41312431

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:38604864 (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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000008 (2/248340, GnomAD_exome)
T=0.000009 (1/111184, ExAC)
A=0.003 (1/376, PharmGKB)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SCN5A : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 248340 C=0.999992 T=0.000008
gnomAD - Exomes European Sub 134076 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 48392 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34402 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 15402 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10038 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6030 C=1.0000 T=0.0000
ExAC Global Study-wide 111184 C=0.999991 T=0.000009
ExAC Europe Sub 68214 C=0.99999 T=0.00001
ExAC Asian Sub 22818 C=1.00000 T=0.00000
ExAC American Sub 10380 C=1.00000 T=0.00000
ExAC African Sub 8940 C=1.0000 T=0.0000
ExAC Other Sub 832 C=1.000 T=0.000
PharmGKB Aggregated Global Study-wide 376 C=0.997 A=0.003
PharmGKB Aggregated PA164153182 Sub 376 C=0.997 A=0.003
Help

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.38604864C>A
GRCh38.p14 chr 3 NC_000003.12:g.38604864C>T
GRCh37.p13 chr 3 NC_000003.11:g.38646355C>A
GRCh37.p13 chr 3 NC_000003.11:g.38646355C>T
SCN5A RefSeqGene (LRG_289) NG_008934.1:g.49809G>T
SCN5A RefSeqGene (LRG_289) NG_008934.1:g.49809G>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.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform g NP_001341630.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 7 NM_001354701.2:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform g NP_001341630.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant 5 NM_001160160.2:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform e NP_001153632.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 5 NM_001160160.2:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform e NP_001153632.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant 2 NM_000335.5:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform b NP_000326.2:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 2 NM_000335.5:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform b NP_000326.2:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant 4 NM_001099405.2:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform d NP_001092875.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 4 NM_001099405.2:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform d NP_001092875.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant 3 NM_001099404.2:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform c NP_001092874.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 3 NM_001099404.2:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform c NP_001092874.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant 6 NM_001160161.2:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform f NP_001153633.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 6 NM_001160161.2:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform f NP_001153633.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant 1 NM_198056.3:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform a NP_932173.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant 1 NM_198056.3:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform a NP_932173.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
SCN5A transcript variant X1 XM_011533991.3:c.1383G>T L [TTG] > F [TTT] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform X1 XP_011532293.1:p.Leu461Phe L (Leu) > F (Phe) Missense Variant
SCN5A transcript variant X1 XM_011533991.3:c.1383G>A L [TTG] > L [TTA] Coding Sequence Variant
sodium channel protein type 5 subunit alpha isoform X1 XP_011532293.1:p.Leu461= L (Leu) > L (Leu) Synonymous Variant
Help

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
Help

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 T
GRCh38.p14 chr 3 NC_000003.12:g.38604864= NC_000003.12:g.38604864C>A NC_000003.12:g.38604864C>T
GRCh37.p13 chr 3 NC_000003.11:g.38646355= NC_000003.11:g.38646355C>A NC_000003.11:g.38646355C>T
SCN5A RefSeqGene (LRG_289) NG_008934.1:g.49809= NG_008934.1:g.49809G>T NG_008934.1:g.49809G>A
SCN5A transcript variant 2 NM_000335.5:c.1383= NM_000335.5:c.1383G>T NM_000335.5:c.1383G>A
SCN5A transcript variant 2 NM_000335.4:c.1383= NM_000335.4:c.1383G>T NM_000335.4:c.1383G>A
SCN5A transcript variant 1 NM_198056.3:c.1383= NM_198056.3:c.1383G>T NM_198056.3:c.1383G>A
SCN5A transcript variant 1 NM_198056.2:c.1383= NM_198056.2:c.1383G>T NM_198056.2:c.1383G>A
SCN5A transcript variant 3 NM_001099404.2:c.1383= NM_001099404.2:c.1383G>T NM_001099404.2:c.1383G>A
SCN5A transcript variant 3 NM_001099404.1:c.1383= NM_001099404.1:c.1383G>T NM_001099404.1:c.1383G>A
SCN5A transcript variant 4 NM_001099405.2:c.1383= NM_001099405.2:c.1383G>T NM_001099405.2:c.1383G>A
SCN5A transcript variant 4 NM_001099405.1:c.1383= NM_001099405.1:c.1383G>T NM_001099405.1:c.1383G>A
SCN5A transcript variant 7 NM_001354701.2:c.1383= NM_001354701.2:c.1383G>T NM_001354701.2:c.1383G>A
SCN5A transcript variant 7 NM_001354701.1:c.1383= NM_001354701.1:c.1383G>T NM_001354701.1:c.1383G>A
SCN5A transcript variant 5 NM_001160160.2:c.1383= NM_001160160.2:c.1383G>T NM_001160160.2:c.1383G>A
SCN5A transcript variant 5 NM_001160160.1:c.1383= NM_001160160.1:c.1383G>T NM_001160160.1:c.1383G>A
SCN5A transcript variant 6 NM_001160161.2:c.1383= NM_001160161.2:c.1383G>T NM_001160161.2:c.1383G>A
SCN5A transcript variant 6 NM_001160161.1:c.1383= NM_001160161.1:c.1383G>T NM_001160161.1:c.1383G>A
SCN5A transcript variant 11 NR_176299.1:n.2129= NR_176299.1:n.2129G>T NR_176299.1:n.2129G>A
SCN5A transcript variant 8 NM_001407185.1:c.1383= NM_001407185.1:c.1383G>T NM_001407185.1:c.1383G>A
SCN5A transcript variant X1 XM_011533991.3:c.1383= XM_011533991.3:c.1383G>T XM_011533991.3:c.1383G>A
SCN5A transcript variant X1 XM_011533991.2:c.1383= XM_011533991.2:c.1383G>T XM_011533991.2:c.1383G>A
SCN5A transcript variant X2 XM_011533991.1:c.1383= XM_011533991.1:c.1383G>T XM_011533991.1:c.1383G>A
sodium channel protein type 5 subunit alpha isoform b NP_000326.2:p.Leu461= NP_000326.2:p.Leu461Phe NP_000326.2:p.Leu461=
sodium channel protein type 5 subunit alpha isoform a NP_932173.1:p.Leu461= NP_932173.1:p.Leu461Phe NP_932173.1:p.Leu461=
sodium channel protein type 5 subunit alpha isoform c NP_001092874.1:p.Leu461= NP_001092874.1:p.Leu461Phe NP_001092874.1:p.Leu461=
sodium channel protein type 5 subunit alpha isoform d NP_001092875.1:p.Leu461= NP_001092875.1:p.Leu461Phe NP_001092875.1:p.Leu461=
sodium channel protein type 5 subunit alpha isoform g NP_001341630.1:p.Leu461= NP_001341630.1:p.Leu461Phe NP_001341630.1:p.Leu461=
sodium channel protein type 5 subunit alpha isoform e NP_001153632.1:p.Leu461= NP_001153632.1:p.Leu461Phe NP_001153632.1:p.Leu461=
sodium channel protein type 5 subunit alpha isoform f NP_001153633.1:p.Leu461= NP_001153633.1:p.Leu461Phe NP_001153633.1:p.Leu461=
sodium channel protein type 5 subunit alpha isoform X1 XP_011532293.1:p.Leu461= XP_011532293.1:p.Leu461Phe XP_011532293.1:p.Leu461=
Help

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#.

5 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 RSG_JCVI ss65625695 Oct 18, 2006 (127)
2 RSG_UW ss70458671 May 17, 2007 (127)
3 PHARMGKB_PAT ss290491899 May 09, 2011 (134)
4 EVA_EXAC ss1686933430 Apr 01, 2015 (144)
5 GNOMAD ss2733640184 Nov 08, 2017 (151)
6 ExAC NC_000003.11 - 38646355 Oct 12, 2018 (152)
7 gnomAD - Exomes NC_000003.11 - 38646355 Jul 13, 2019 (153)
8 PharmGKB Aggregated NC_000003.12 - 38604864 Apr 25, 2020 (154)
Help

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
8245 NC_000003.12:38604863:C:A NC_000003.12:38604863:C:A (self)
ss65625695, ss70458671, ss290491899 NT_022517.18:38586354:C:A NC_000003.12:38604863:C:A (self)
6852600, 2715073, ss1686933430, ss2733640184 NC_000003.11:38646354:C:T NC_000003.12:38604863:C:T (self)
Help

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

No publications for rs41312431

Help

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.

Software version is: 2.0.1.post761+d5e8e07