NM_000334.4(SCN4A):c.4764C>A (p.Ile1588=) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 22, 2018
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:: RCV000579024.1

Allele description [Variation Report for NM_000334.4(SCN4A):c.4764C>A (p.Ile1588=)]

NM_000334.4(SCN4A):c.4764C>A (p.Ile1588=)

Genes:

GH-LCR:growth hormone locus control region [Gene]
SCN4A:sodium voltage-gated channel alpha subunit 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q23.3

Genomic location:

Preferred name:

NM_000334.4(SCN4A):c.4764C>A (p.Ile1588=)

HGVS:

NC_000017.11:g.63941518G>T
NG_011699.1:g.36401C>A
NG_042788.1:g.24426G>T
NM_000334.4:c.4764C>AMANE SELECT
NP_000325.4:p.Ile1588=
NC_000017.10:g.62018878G>T

Links:

dbSNP: rs768778696

NCBI 1000 Genomes Browser:

rs768778696

Molecular consequence:

NM_000334.4:c.4764C>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000681367	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jan 22, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000681367

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jan 22, 2018)

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, SCV000681367.1

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

Description

A variant of uncertain significance has been identified in the SCN4A gene. The c.4764 C>A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.4764 C>A variant is not observed in large population cohorts (Lek et al., 2016). Several in silico splice prediction models predict that c.4764 C>A creates a cryptic splice acceptor site which may supplant the natural splice acceptor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	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: Apr 23, 2022

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