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NM_000553.6(WRN):c.4216C>T (p.Arg1406Ter)

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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:
Dec 8, 2020
Accession:
VCV000135443.6
Variation ID:
135443
Description:
single nucleotide variant
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NM_000553.6(WRN):c.4216C>T (p.Arg1406Ter)

Allele ID
139182
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p12
Genomic location
8: 31173019 (GRCh38) GRCh38 UCSC
8: 31030535 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.31030535C>T
NC_000008.11:g.31173019C>T
NM_000553.6:c.4216C>T MANE Select NP_000544.2:p.Arg1406Ter nonsense
... more HGVS
Protein change
R1406*
Other names
-
Canonical SPDI
NC_000008.11:31173018:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00539 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00346
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00077
1000 Genomes Project 0.00539
Trans-Omics for Precision Medicine (TOPMed) 0.00127
The Genome Aggregation Database (gnomAD) 0.00118
The Genome Aggregation Database (gnomAD), exomes 0.00305
Links
ClinGen: CA162779
dbSNP: rs11574410
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 Dec 8, 2020 RCV000988046.4
Benign 2 criteria provided, single submitter Dec 30, 2014 RCV000122300.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WRN - - GRCh38
GRCh37
1881 1944

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Werner syndrome
Allele origin: unknown
Mendelics
Accession: SCV001137606.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Werner syndrome
Allele origin: germline
Invitae
Accession: SCV000285575.7
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Dec 30, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229774.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://exac.broadinstitute.org/g…
http://www.ncbi.nlm.nih.gov/vari…
http://www.pathology.washington.…
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Werner syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001325808.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000086528.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

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
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327
http://exac.broadinstitute.org/gene/ENSG00000165392 - - - -
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=WRN - - - -
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=8&from=31030535&to=31030535 - - - -
http://www.pathology.washington.edu/research/werner/database/ - - - -

Text-mined citations for rs11574410...

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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 Jun 14, 2021