NM_001365536.1(SCN9A):c.4206+3A>G AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 26, 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:: RCV002327634.2

Allele description [Variation Report for NM_001365536.1(SCN9A):c.4206+3A>G]

NM_001365536.1(SCN9A):c.4206+3A>G

Genes:

SCN1A-AS1:SCN1A and SCN9A antisense RNA 1 [Gene - HGNC]
SCN9A:sodium voltage-gated channel alpha subunit 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001365536.1(SCN9A):c.4206+3A>G

HGVS:

NC_000002.12:g.166228688T>C
NG_012798.1:g.152300A>G
NM_001365536.1:c.4206+3A>GMANE SELECT
NM_002977.4:c.4173+3A>G
LRG_369t1:c.4173+3A>G
LRG_369:g.152300A>G
NC_000002.11:g.167085198T>C
NM_002977.3:c.4173+3A>G

Links:

dbSNP: rs1694951853

NCBI 1000 Genomes Browser:

rs1694951853

Molecular consequence:

NM_001365536.1:c.4206+3A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_002977.4:c.4173+3A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002630506	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 26, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002630506

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 26, 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 Ambry Genetics, SCV002630506.2

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

Description

The c.4173+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 21 in the SCN9A gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: Sep 29, 2024

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