NM_001165963.4(SCN1A):c.3879+5G>T AND Severe myoclonic epilepsy in infancy

Germline classification:: Uncertain significance (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003339537.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3879+5G>T]

NM_001165963.4(SCN1A):c.3879+5G>T

Genes:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.3879+5G>T

HGVS:

NC_000002.12:g.166012104C>A
NG_011906.1:g.66536G>T
NM_001165963.3:c.3879+5G>T
NM_001165963.4:c.3879+5G>TMANE SELECT
NM_001165964.3:c.3795+5G>T
NM_001202435.3:c.3879+5G>T
NM_001353948.2:c.3879+5G>T
NM_001353949.2:c.3846+5G>T
NM_001353950.2:c.3846+5G>T
NM_001353951.2:c.3846+5G>T
NM_001353952.2:c.3846+5G>T
NM_001353954.2:c.3843+5G>T
NM_001353955.2:c.3843+5G>T
NM_001353957.2:c.3795+5G>T
NM_001353958.2:c.3795+5G>T
NM_001353960.2:c.3792+5G>T
NM_001353961.2:c.1437+5G>T
NM_006920.6:c.3846+5G>T
LRG_8:g.66536G>T
NC_000002.11:g.166868614C>A
NM_001165963.1:c.3879+5G>T
NM_001165963.4:c.3879+5G>T

Links:

dbSNP: rs796052999

NCBI 1000 Genomes Browser:

rs796052999

Molecular consequence:

NM_001165963.4:c.3879+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001165964.3:c.3795+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001202435.3:c.3879+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353948.2:c.3879+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353949.2:c.3846+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353950.2:c.3846+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353951.2:c.3846+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353952.2:c.3846+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353954.2:c.3843+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353955.2:c.3843+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353957.2:c.3795+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353958.2:c.3795+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353960.2:c.3792+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001353961.2:c.1437+5G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_006920.6:c.3846+5G>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Severe myoclonic epilepsy in infancy (DRVT)
Synonyms:: Epilepsy, Myoclonic, Infantile, Severe; Dravet syndrome; Epileptic encephalopathy, early infantile, 6 (Dravet syndrome); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100135; MedGen: C0751122; Orphanet: 33069; OMIM: 607208

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004047265	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004047265

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047265.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The splice site variant c.3879+5G>T in SCN1A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has been reported to the ClinVar database as Uncertain_significance. The c.3879+5G>T variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant does not affect an invariant splice nucleotide and hence functional studies will be require to demonstrate exon skipping. For these reasons the variant has been classified as Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

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