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NM_144573.4(NEXN):c.1408G>C (p.Glu470Gln)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Oct 4, 2021)
Last evaluated:
Nov 28, 2020
Accession:
VCV000138511.10
Variation ID:
138511
Description:
single nucleotide variant
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NM_144573.4(NEXN):c.1408G>C (p.Glu470Gln)

Allele ID
142214
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p31.1
Genomic location
1: 77935979 (GRCh38) GRCh38 UCSC
1: 78401664 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_144573.3:c.1408G>C NP_653174.3:p.Glu470Gln missense
NC_000001.10:g.78401664G>C
NC_000001.11:g.77935979G>C
... more HGVS
Protein change
E470Q, E406Q
Other names
p.E470Q:GAG>CAG
Canonical SPDI
NC_000001.11:77935978:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00240 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00061
The Genome Aggregation Database (gnomAD) 0.00249
Trans-Omics for Precision Medicine (TOPMed) 0.00286
1000 Genomes Project 0.00240
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00315
Exome Aggregation Consortium (ExAC) 0.00083
Links
dbSNP: rs35366555
ClinGen: CA181124
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts Mar 14, 2014 RCV000154659.4
Benign 1 criteria provided, single submitter Nov 28, 2020 RCV000204884.7
Benign 1 criteria provided, single submitter Oct 1, 2015 RCV000245536.1
Benign 1 criteria provided, single submitter Nov 2, 2017 RCV001170729.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NEXN - - GRCh38
GRCh37
359 381

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 14, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000170747.10
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)
Benign
(Jul 18, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000204336.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Glu470Gln in exon 11 of NEXN: This variant is not expected to have clinical sign ificance because it has been identified in 1.0% (36/3586) of … (more)
Benign
(Oct 01, 2015)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000320172.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Nov 28, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1CC
Familial hypertrophic cardiomyopathy 20
Allele origin: germline
Invitae
Accession: SCV000260567.7
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 02, 2017)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Accession: SCV001333332.1
Submitted: (Mar 03, 2020)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001917567.1
Submitted: (Sep 23, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001962932.1
Submitted: (Oct 04, 2021)
Evidence details

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs35366555...

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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 Oct 24, 2021