NM_001165963.4(SCN1A):c.1662+1G>A AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 9, 2023
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:: RCV000521007.3

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1662+1G>A]

NM_001165963.4(SCN1A):c.1662+1G>A

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.1662+1G>A

HGVS:

NC_000002.12:g.166045042C>T
NG_011906.1:g.33598G>A
NM_001165963.4:c.1662+1G>AMANE SELECT
NM_001165964.3:c.1662+1G>A
NM_001202435.3:c.1662+1G>A
NM_001353948.2:c.1662+1G>A
NM_001353949.2:c.1662+1G>A
NM_001353950.2:c.1662+1G>A
NM_001353951.2:c.1662+1G>A
NM_001353952.2:c.1662+1G>A
NM_001353954.2:c.1659+1G>A
NM_001353955.2:c.1659+1G>A
NM_001353957.2:c.1662+1G>A
NM_001353958.2:c.1662+1G>A
NM_001353960.2:c.1659+1G>A
NM_001353961.2:c.-764+1G>A
NM_006920.6:c.1662+1G>A
LRG_8:g.33598G>A
NC_000002.11:g.166901552C>T
NM_001165963.1:c.1662+1G>A

Links:

dbSNP: rs794726749

NCBI 1000 Genomes Browser:

rs794726749

Molecular consequence:

NM_001165963.4:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001165964.3:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001202435.3:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353948.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353949.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353950.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353951.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353952.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353954.2:c.1659+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353955.2:c.1659+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353957.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353958.2:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353960.2:c.1659+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353961.2:c.-764+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_006920.6:c.1662+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000616865	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 9, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000616865

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 9, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000616865.3

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

Description

Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); Has not been previously published as pathogenic or benign to our knowledge; Lost residues are within the cytoplasmic loop between the first and second homologous domains; This variant is associated with the following publications: (PMID: 17054684)

#	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

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