NM_001037.5(SCN1B):c.267C>T (p.Arg89=) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jun 30, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000586689.20

Allele description [Variation Report for NM_001037.5(SCN1B):c.267C>T (p.Arg89=)]

NM_001037.5(SCN1B):c.267C>T (p.Arg89=)

Gene:

SCN1B:sodium voltage-gated channel beta subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.11

Genomic location:

Preferred name:

NM_001037.5(SCN1B):c.267C>T (p.Arg89=)

Other names:

p.R89R:CGC>CGT

HGVS:

NC_000019.10:g.35033558C>T
NG_013359.1:g.7871C>T
NM_001037.5:c.267C>TMANE SELECT
NM_001321605.2:c.168C>T
NM_199037.5:c.267C>T
NP_001028.1:p.Arg89=
NP_001308534.1:p.Arg56=
NP_950238.1:p.Arg89=
LRG_420t1:c.267C>T
LRG_420:g.7871C>T
LRG_420p1:p.Arg89=
NC_000019.9:g.35524462C>T
NM_001037.3:c.267C>T
NM_001037.4:c.267C>T
NM_199037.3:c.267C>T
p.Arg89Arg

Links:

dbSNP: rs140949982

NCBI 1000 Genomes Browser:

rs140949982

Molecular consequence:

NM_001037.5:c.267C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001321605.2:c.168C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_199037.5:c.267C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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
SCV000700046	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (May 16, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001928504	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002498456	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Mar 1, 2022)	germline	clinical testing	Citation Link,
SCV003800004	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Likely benign (Jun 30, 2022)	germline	clinical testing	Citation Link

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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
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, SCV000700046.1

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

Description

Variant summary: The SCN1B c.267C>T (p.Arg89=) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 4/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. This variant was found in 85/121400 control chromosomes at a frequency of 0.0007002, which is approximately 70 times of the estimated maximal allele frequency of a pathogenic SCN1B variant (0.00001), suggesting this variant is a benign polymorphism. The variant was found to co-occure with a pathogenic variant, c.573_577delGCGCT in KCNH2, further suggesting non-pathogenic nature of the variant of interest. In addition, several clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as 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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001928504.1

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

From CeGaT Center for Human Genetics Tuebingen, SCV002498456.13

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

Description

SCN1B: BP4, BP7

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003800004.2

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

Last Updated: Jun 2, 2024

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