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NM_144573.4(NEXN):c.363G>A (p.Thr121=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000047906.12
Variation ID:
47906
Description:
single nucleotide variant
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NM_144573.4(NEXN):c.363G>A (p.Thr121=)

Allele ID
57070
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p31.1
Genomic location
1: 77918189 (GRCh38) GRCh38 UCSC
1: 78383874 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.78383874G>A
NC_000001.11:g.77918189G>A
NG_016625.1:g.34675G>A
... more HGVS
Protein change
-
Other names
p.T121T:ACG>ACA
Canonical SPDI
NC_000001.11:77918188:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01278 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00295
Exome Aggregation Consortium (ExAC) 0.00373
The Genome Aggregation Database (gnomAD) 0.01166
1000 Genomes Project 0.01278
Trans-Omics for Precision Medicine (TOPMed) 0.01295
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01339
Links
ClinGen: CA142155
dbSNP: rs35117963
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 5 criteria provided, multiple submitters, no conflicts Jul 8, 2013 RCV000041177.6
Benign 1 criteria provided, single submitter Jul 8, 2015 RCV000242769.1
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV000231898.7
Benign 1 criteria provided, single submitter Jun 3, 2016 RCV000768800.1
Benign 1 criteria provided, single submitter Mar 18, 2020 RCV001284866.1
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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
357 379

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 08, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000170744.10
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
(Jun 03, 2016)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Study: Canadian Open Genetics Repository
Accession: SCV000900172.1
Submitted: (Apr 30, 2018)
Evidence details
Benign
(May 22, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000064868.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
3.8% (119/3092) Afr Amer chrom (ESP)
Benign
(Jul 08, 2015)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000318797.5
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
Benign
(Mar 18, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001470959.1
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1CC
Familial hypertrophic cardiomyopathy 20
Allele origin: germline
Invitae
Accession: SCV000291371.7
Submitted: (Jan 07, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001968010.1
Submitted: (Sep 21, 2021)
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: SCV001924224.1
Submitted: (Sep 23, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001958852.1
Submitted: (Sep 30, 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 rs35117963...

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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 07, 2021