NM_000742.4(CHRNA2):c.140C>T (p.Thr47Met) AND Epilepsy, nocturnal frontal lobe, type 4

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting classifications of pathogenicity (4 submissions)
Last evaluated:: May 28, 2019
Review status:: criteria provided, conflicting classifications

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:: RCV000615228.3

Allele description

NM_000742.4(CHRNA2):c.140C>T (p.Thr47Met)

Gene:

CHRNA2:cholinergic receptor nicotinic alpha 2 subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8p21.2

Genomic location:

Preferred name:

NM_000742.4(CHRNA2):c.140C>T (p.Thr47Met)

Other names:

p.T47M:ACG>ATG

HGVS:

NC_000008.11:g.27469915G>A
NG_015827.1:g.14382C>T
NM_000742.4:c.140C>TMANE SELECT
NM_001282455.2:c.140C>T
NM_001347705.2:c.-288C>T
NM_001347706.2:c.-333C>T
NM_001347707.2:c.-274C>T
NM_001347708.2:c.-322C>T
NP_000733.2:p.Thr47Met
NP_001269384.1:p.Thr47Met
NC_000008.10:g.27327432G>A
NM_000742.3:c.140C>T

Protein change:

T47M

Links:

dbSNP: rs74772771

NCBI 1000 Genomes Browser:

rs74772771

Molecular consequence:

NM_001347705.2:c.-288C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001347706.2:c.-333C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001347707.2:c.-274C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001347708.2:c.-322C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000742.4:c.140C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001282455.2:c.140C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Epilepsy, nocturnal frontal lobe, type 4 (ENFL4)
Synonyms:: EPILEPSY, FAMILIAL, WITH NOCTURNAL WANDERING AND ICTAL FEAR; Autosomal dominant nocturnal frontal lobe epilepsy type 4
Identifiers:: MONDO: MONDO:0012474; MedGen: C1835905; Orphanet: 98784; OMIM: 610353

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000734602	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000743961	Genome Diagnostics Laboratory,University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Jul 28, 2017)	germline	clinical testing	Citation Link,
SCV001137599	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Uncertain significance (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001327005	Illumina Clinical Services Laboratory,Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 12, 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
not provided	unknown	unknown	not provided	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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000734602.1

#	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 Genome Diagnostics Laboratory,University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743961.1

#	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 Mendelics, SCV001137599.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Clinical Services Laboratory,Illumina, SCV001327005.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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: Jul 10, 2021

ClinVar

Relating variation to medicine