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NM_144573.4(NEXN):c.156C>T (p.Asp52=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 2, 2020
Accession:
VCV000226849.8
Variation ID:
226849
Description:
single nucleotide variant
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NM_144573.4(NEXN):c.156C>T (p.Asp52=)

Allele ID
228514
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p31.1
Genomic location
1: 77917694 (GRCh38) GRCh38 UCSC
1: 78383379 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.78383379C>T
NC_000001.11:g.77917694C>T
NM_144573.4:c.156C>T MANE Select NP_653174.3:p.Asp52= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:77917693:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
1000 Genomes Project 0.00060
Exome Aggregation Consortium (ExAC) 0.00038
Trans-Omics for Precision Medicine (TOPMed) 0.00118
The Genome Aggregation Database (gnomAD), exomes 0.00030
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00076
The Genome Aggregation Database (gnomAD) 0.00125
Links
ClinGen: CA918569
dbSNP: rs371431782
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Apr 7, 2015 RCV000223646.2
Benign 1 criteria provided, single submitter Nov 2, 2020 RCV000465499.6
Likely benign 1 criteria provided, single submitter Sep 10, 2015 RCV000622079.1
Benign 1 criteria provided, single submitter Mar 29, 2018 RCV001170495.1
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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
352 374

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 07, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000513923.4
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
(Mar 21, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000269444.3
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Asp52Asp in exon 3 of NEXN: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, … (more)
Benign
(Mar 29, 2018)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Accession: SCV001333078.1
Submitted: (Mar 03, 2020)
Evidence details
Likely benign
(Sep 10, 2015)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000737363.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Benign
(Nov 02, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1CC
Familial hypertrophic cardiomyopathy 20
Allele origin: germline
Invitae
Accession: SCV000560167.6
Submitted: (Jan 07, 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 rs371431782...

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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 Jul 07, 2021