NM_174934.4(SCN4B):c.480C>G (p.Asn160Lys) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 15, 2021
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:: RCV001806761.1

Allele description [Variation Report for NM_174934.4(SCN4B):c.480C>G (p.Asn160Lys)]

NM_174934.4(SCN4B):c.480C>G (p.Asn160Lys)

Gene:

SCN4B:sodium voltage-gated channel beta subunit 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_174934.4(SCN4B):c.480C>G (p.Asn160Lys)

HGVS:

NC_000011.10:g.118141320G>C
NG_011710.1:g.16596C>G
NM_001142348.2:c.78C>G
NM_001142349.2:c.150C>G
NM_174934.4:c.480C>GMANE SELECT
NP_001135820.1:p.Asn26Lys
NP_001135821.1:p.Asn50Lys
NP_777594.1:p.Asn160Lys
LRG_330t1:c.480C>G
LRG_330:g.16596C>G
NC_000011.9:g.118012035G>C
NM_174934.3:c.480C>G
NR_024527.2:n.469C>G

Protein change:

N160K

Links:

dbSNP: rs72546675

NCBI 1000 Genomes Browser:

rs72546675

Molecular consequence:

NM_001142348.2:c.78C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001142349.2:c.150C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_174934.4:c.480C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_024527.2:n.469C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV002051147	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Dec 15, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002051147

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Dec 15, 2021)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002051147.1

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

Description

Variant summary: SCN4B c.480C>G (p.Asn160Lys) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 251412 control chromosomes, predominantly at a frequency of 0.0004 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 136 fold of the estimated maximal expected allele frequency for a pathogenic variant in SCN4B causing Long QT Syndrome phenotype (2.9e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. To our knowledge, no occurrence of c.480C>G in individuals affected with Long QT Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely benign.

#	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		not provided	not provided	not provided	not provided

Last Updated: Aug 11, 2024

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