NM_000080.4(CHRNE):c.53G>T (p.Gly18Val) AND not specified

Germline classification:: Benign (5 submissions)
Last evaluated:: Apr 19, 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:: RCV000116741.18

Allele description [Variation Report for NM_000080.4(CHRNE):c.53G>T (p.Gly18Val)]

NM_000080.4(CHRNE):c.53G>T (p.Gly18Val)

Genes:

CHRNE:cholinergic receptor nicotinic epsilon subunit [Gene - OMIM - HGNC]
C17orf107:chromosome 17 open reading frame 107 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_000080.4(CHRNE):c.53G>T (p.Gly18Val)

HGVS:

NC_000017.11:g.4902757C>A
NG_008029.2:g.5319G>T
NG_135291.1:g.406C>A
NM_000080.4:c.53G>TMANE SELECT
NM_001145536.2:c.*2224C>AMANE SELECT
NP_000071.1:p.Gly18Val
LRG_1254t1:c.53G>T
LRG_1254:g.5319G>T
LRG_1254p1:p.Gly18Val
NC_000017.10:g.4806052C>A
NM_000080.3:c.53G>T
Q04844:p.Gly18Val

Protein change:

G18V

Links:

UniProtKB: Q04844#VAR_048170; dbSNP: rs4790235

NCBI 1000 Genomes Browser:

rs4790235

Molecular consequence:

NM_001145536.2:c.*2224C>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000080.4:c.53G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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MULTISPECIES: VEB family extended-spectrum class A beta-lactamase [Morganellacea...
MULTISPECIES: VEB family extended-spectrum class A beta-lactamase [Morganellaceae]
gi|2735537685|ref|WP_346819020.1|

Protein
MULTISPECIES: hypothetical protein [Providencia]
MULTISPECIES: hypothetical protein [Providencia]
gi|2784780924|ref|WP_369473553.1|

Protein
Arabidopsis thaliana UDP-glucose:flavonoid 3-o-glucosyltransferase (UF3GT), mRNA
Arabidopsis thaliana UDP-glucose:flavonoid 3-o-glucosyltransferase (UF3GT), mRNA
gi|1063741164|ref|NM_124785.3|

Nucleotide
Excinuclease ABC, C subunit, N-terminal [Arabidopsis thaliana]
Excinuclease ABC, C subunit, N-terminal [Arabidopsis thaliana]
gi|42569467|ref|NP_180594.2|

Protein
Uncultured Bellilinea sp. clone 37-160B-CB139 16S ribosomal RNA gene, partial se...
Uncultured Bellilinea sp. clone 37-160B-CB139 16S ribosomal RNA gene, partial sequence
gi|1215529599|gb|MF470667.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000150715	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Benign (Aug 15, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000301946	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000519232	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jul 8, 2016)	germline	clinical testing	Citation Link,
SCV000966273	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Apr 19, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001959375	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

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
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

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

See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000150715.1

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

#	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

From PreventionGenetics, part of Exact Sciences, SCV000301946.1

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

#	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

From GeneDx, SCV000519232.4

#	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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000966273.1

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

Description

p.Gly18Val in exon 2 of CHRNE: This variant is classified as benign because it h as been identified in 23% (7902/34416) of Latino chromosomes, including 1073 hom ozygous individuals, by the Genome Aggregation Database (gnomAD, http://gnomad.b roadinstitute.org; dbSNP rs4790235).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001959375.1

#	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

Last Updated: Sep 29, 2024

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