NM_001165963.4(SCN1A):c.3879+5G>A AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jun 1, 2016
Review status:: criteria provided, conflicting classifications

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:: RCV000188930.26

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

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

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>A

HGVS:

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

Links:

dbSNP: rs796052999

NCBI 1000 Genomes Browser:

rs796052999

Molecular consequence:

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

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000242561	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Aug 6, 2013)	germline	clinical testing	Citation Link,
SCV000575248	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Jun 1, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000242561

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Aug 6, 2013)

germline

clinical testing

Citation Link,

SCV000575248

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Jun 1, 2016)

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	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000242561.11

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

Description

c.3879+5 G>A: IVS19+5 G>A in intron 19 of the SCN1A gene (NM_001165963.1) The c.3879+5 G>A variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. One in silico model predicts it could potentially destroy the natural splice donor site in intron 19. The c.3879+5 G>A sequence change is a strong candidate for a disease-causing mutation; however, in the absence of RNA/functional studies the actual effect of this change is unknown, and the possibility that it is a benign variant cannot be excluded. The variant is found in EPILEPSY panel(s).

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV000575248.32

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

#	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		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine