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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs199474708

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:46858426 (GRCh38.p7) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00000 (1/245902, GnomAD)
C=0.00002 (2/125568, TOPMED)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MYL3 : Missense Variant
Publications
2 citations
Genomic View
See rs on genome
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.p7 chr 3 NC_000003.12:g.46858426T>C
GRCh37.p13 chr 3 NC_000003.11:g.46899916T>C
MYL3 RefSeqGene (LRG_395) NG_007555.2:g.28744A>G
Gene: MYL3, myosin light chain 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MYL3 transcript NM_000258.2:c.517A>G M [ATG] > V [GTG] Coding Sequence Variant
myosin light chain 3 NP_000249.1:p.Met...

NP_000249.1:p.Met173Val

M (Met) > V (Val) Missense 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.

Allele: C (allele ID: 40439 )
ClinVar Accession Disease Names Clinical Significance
RCV000024470.1 not provided Not-Provided
RCV000036029.3 not specified Uncertain-Significance
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").

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Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 245902 T=1.00000 C=0.00000
The Genome Aggregation Database European Sub 133664 T=0.99999 C=0.00001
The Genome Aggregation Database Asian Sub 48030 T=1.0000 C=0.0000
The Genome Aggregation Database American Sub 33580 T=1.0000 C=0.0000
The Genome Aggregation Database African Sub 15302 T=1.0000 C=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9846 T=1.000 C=0.000
The Genome Aggregation Database Other Sub 5480 T=1.000 C=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.99998 C=0.00002
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 T= C Note
GRCh38.p7 chr 3 NC_000003.12:g.46858426T= NC_000003.12:g.46858426T>C
GRCh37.p13 chr 3 NC_000003.11:g.46899916T= NC_000003.11:g.46899916T>C
MYL3 RefSeqGene (LRG_395) NG_007555.2:g.28744A= NG_007555.2:g.28744A>G
MYL3 transcript NM_000258.2:c.517A= NM_000258.2:c.517A>G
myosin light chain 3 NP_000249.1:p.Met173= NP_000249.1:p.Met173Val
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#.

2 ClinVar, 2 Frequency, 6 SubSNP submissions
No Submitter Submission ID Date (Build)
1 LUMC-LOVD ss500610869 Mar 22, 2012 (136)
2 EVA_MGP ss1711015773 Apr 01, 2015 (144)
3 EVA_MCP ss1815616663 Sep 08, 2015 (146)
4 HUMAN_LONGEVITY ss2251208748 Dec 20, 2016 (150)
5 GNOMAD ss2733697153 Nov 08, 2017 (151)
6 TOPMED ss3389376614 Nov 08, 2017 (151)
7 The Genome Aggregation Database NC_000003.11 - 46899916 Jul 20, 2018 (151)
8 Trans-Omics for Precision Medicine NC_000003.12 - 46858426 Jul 20, 2018 (151)
9 ClinVar RCV000024470.1 Jul 20, 2018 (151)
10 ClinVar RCV000036029.3 Jul 20, 2018 (151)
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
2711888, ss1711015773, ss1815616663, ss2733697153 NC_000003.11:46899915:T= NC_000003.12:46858425:T= (self)
250265190, ss500610869, ss2251208748, ss3389376614 NC_000003.12:46858425:T= NC_000003.12:46858425:T= (self)
2711888, ss1711015773, ss1815616663, ss2733697153 NC_000003.11:46899915:T>C NC_000003.12:46858425:T>C (self)
RCV000024470.1, RCV000036029.3, 250265190, ss500610869, ss2251208748, ss3389376614 NC_000003.12:46858425:T>C NC_000003.12:46858425:T>C (self)
Help

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

2 citations for rs199474708
PMID Title Author Year Journal
18403758 Shared genetic causes of cardiac hypertrophy in children and adults. Morita H et al. 2008 The New England journal of medicine
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics

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: 0.1.4.post833+d3ba21e