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NM_001040142.2(SCN2A):c.4446+9A>G AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 7, 2014
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:
RCV000189153.2

Allele description [Variation Report for NM_001040142.2(SCN2A):c.4446+9A>G]

NM_001040142.2(SCN2A):c.4446+9A>G

Gene:
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001040142.2(SCN2A):c.4446+9A>G
HGVS:
  • NC_000002.12:g.165380738A>G
  • NG_008143.1:g.146337A>G
  • NM_001040142.2:c.4446+9A>GMANE SELECT
  • NM_001040143.2:c.4446+9A>G
  • NM_001371246.1:c.4446+9A>G
  • NM_001371247.1:c.4446+9A>G
  • NM_021007.3:c.4446+9A>G
  • NC_000002.11:g.166237248A>G
  • NM_021007.2:c.4446+9A>G
Links:
dbSNP: rs796053140
NCBI 1000 Genomes Browser:
rs796053140
Molecular consequence:
  • NM_001040142.2:c.4446+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001040143.2:c.4446+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371246.1:c.4446+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371247.1:c.4446+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_021007.3:c.4446+9A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000242785GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Feb 7, 2014) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000242785.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

c.4446+9 A>G: IVS24+9 A>G in intron 24 of the SCN2A gene (NM_021007.2). The c.4446+9 A>G nucleotide substitution has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In silico splice algorithms predict the c.4446+9 A>G sequence change may create a cryptic donor site that may lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of the c.4446+9 A>G substitution is unknown. This variant has been observed de novo without verified parentage. The variant is found in INFANT-EPI panel(s).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024