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NM_000748.3(CHRNB2):c.1432T>C (p.Phe478Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 21, 2020
Accession:
VCV000158332.8
Variation ID:
158332
Description:
single nucleotide variant
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NM_000748.3(CHRNB2):c.1432T>C (p.Phe478Leu)

Allele ID
167985
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q21.3
Genomic location
1: 154575855 (GRCh38) GRCh38 UCSC
1: 154548331 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.154548331T>C
NC_000001.11:g.154575855T>C
NG_008027.1:g.13075T>C
NM_000748.3:c.1432T>C MANE Select NP_000739.1:p.Phe478Leu missense
Protein change
F478L
Other names
p.F478L:TTC>CTC
Canonical SPDI
NC_000001.11:154575854:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
The Genome Aggregation Database (gnomAD) 0.00061
Trans-Omics for Precision Medicine (TOPMed) 0.00139
Exome Aggregation Consortium (ExAC) 0.00353
The Genome Aggregation Database (gnomAD), exomes 0.00458
Links
ClinGen: CA271354
dbSNP: rs79137415
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Mar 8, 2017 RCV000179341.5
Likely benign 1 criteria provided, single submitter Aug 31, 2017 RCV000513684.4
Benign 1 criteria provided, single submitter Jun 13, 2016 RCV000716091.1
Benign 1 criteria provided, single submitter Nov 21, 2020 RCV001084374.2
Benign 1 criteria provided, single submitter - RCV001258263.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CHRNB2 - - GRCh38
GRCh37
293 371

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 27, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000192827.2
Submitted: (Oct 04, 2017)
Evidence details
Benign
(Mar 08, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000240553.7
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Likely benign
(Oct 10, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231575.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (1)
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 21, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal dominant nocturnal frontal lobe epilepsy
Allele origin: germline
Invitae
Accession: SCV000285620.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Aug 31, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610278.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: research
Epilepsy, nocturnal frontal lobe, type 3
(Autosomal dominant inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001435183.1
Submitted: (Mar 10, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The heterozygous p.Phe478Leu variant in CHRNB2 has been identified in at least 1 individual with unexplained epilepsy (PMID: 21703448), but has also been identified in … (more)
Benign
(Jun 13, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000846924.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Klassen T Cell 2011 PMID: 21703448
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CHRNB2 - - - -

Text-mined citations for rs79137415...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2021