NM_001040142.2(SCN2A):c.-51-61A>G AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jun 14, 2018
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:: RCV000830092.2

Allele description [Variation Report for NM_001040142.2(SCN2A):c.-51-61A>G]

NM_001040142.2(SCN2A):c.-51-61A>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.-51-61A>G

HGVS:

NC_000002.12:g.165295712A>G
NG_008143.1:g.61311A>G
NM_001040142.2:c.-51-61A>GMANE SELECT
NM_001040143.2:c.-51-61A>G
NM_001371246.1:c.-51-61A>G
NM_001371247.1:c.-51-61A>G
NM_021007.3:c.-51-61A>G
NC_000002.11:g.166152222A>G
NM_021007.2:c.-51-61A>G

Links:

dbSNP: rs13407286

NCBI 1000 Genomes Browser:

rs13407286

Molecular consequence:

NM_001040142.2:c.-51-61A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001040143.2:c.-51-61A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371246.1:c.-51-61A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371247.1:c.-51-61A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_021007.3:c.-51-61A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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sulfotransferase [Frankia sp. CgS1]
sulfotransferase [Frankia sp. CgS1]
gi|2741239980|ref|WP_349256640.1|

Protein
MULTISPECIES: glycosyltransferase family 4 protein [Frankia]
MULTISPECIES: glycosyltransferase family 4 protein [Frankia]
gi|499757488|ref|WP_011438222.1|

Protein
NF041680 family putative transposase [Frankia sp. CgS1]
NF041680 family putative transposase [Frankia sp. CgS1]
gi|2741239985|ref|WP_349256645.1|

Protein
IS4 family transposase [Frankia sp. CgS1]
IS4 family transposase [Frankia sp. CgS1]
gi|2741239984|ref|WP_349256644.1|

Protein
Paenibacillus sp. FSL H7-0357 chromosome, complete genome
Paenibacillus sp. FSL H7-0357 chromosome, complete genome
gi|749299172|ref|NZ_CP009241.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000971827	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Jun 14, 2018)	germline	clinical testing	Citation Link,
SCV005256409	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000971827

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Jun 14, 2018)

germline

clinical testing

Citation Link,

SCV005256409

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

PubMed (1)
[See all records that cite this PMID]

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, not provided

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000971827.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005256409.1

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

#	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: Sep 29, 2024

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