NM_000335.5(SCN5A):c.998+5G>A AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 7, 2019
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:: RCV000151802.13

Allele description [Variation Report for NM_000335.5(SCN5A):c.998+5G>A]

NM_000335.5(SCN5A):c.998+5G>A

Gene:

SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.998+5G>A

HGVS:

NC_000003.12:g.38608146C>T
NG_008934.1:g.46527G>A
NM_000335.5:c.998+5G>AMANE SELECT
NM_001099404.2:c.998+5G>A
NM_001099405.2:c.998+5G>A
NM_001160160.2:c.998+5G>A
NM_001160161.2:c.998+5G>A
NM_001354701.2:c.998+5G>A
NM_198056.3:c.998+5G>A
LRG_289t1:c.998+5G>A
LRG_289t3:c.998+5G>A
LRG_289:g.46527G>A
NC_000003.11:g.38649637C>T
NM_001099404.1:c.998+5G>A
NM_198056.2:c.998+5G>A

Links:

dbSNP: rs187531872

NCBI 1000 Genomes Browser:

rs187531872

Molecular consequence:

NM_000335.5:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001099404.2:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001099405.2:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001160160.2:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001160161.2:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354701.2:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_198056.3:c.998+5G>A - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000200265	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Feb 7, 2019)	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

SCV000200265

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Feb 7, 2019)

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	unknown	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000200265.6

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

Description

The 998+5G>A variant in SCN5A has not been reported in individuals with cardiomyopathy, but it has been identified in 1/8366 of European American chromosomes by the NHLBI Exome Sequencing Project and in 0.5% (1/186) of Finnish chromosomes by the 1000 Genomes Project (http://evs.gs.washington.edu/EVS/;dbSNP rs187531872). This variant is located in the 5' splice region. Computational tools suggest a possible impact to splicing. However, this information is not predictive enough to determine pathogenicity. Additional information is needed to fully assess the clinical significance of the 998+5G>A variant. 998+5G>A intron 8 of SCN5A (rs187531872; allele frequency = 1/8366). This variant has been seen by several clinical labs in ClinVar (uncertain significance), and affects splice in silico. This variant has been reported in an individual affected with long QT syndrome (PMID: 23631430).

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

Last Updated: Oct 13, 2024

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