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NM_000553.6(WRN):c.3785C>G (p.Thr1262Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Aug 19, 2021)
Last evaluated:
Apr 20, 2021
Accession:
VCV000135436.15
Variation ID:
135436
Description:
single nucleotide variant
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NM_000553.6(WRN):c.3785C>G (p.Thr1262Arg)

Allele ID
139175
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p12
Genomic location
8: 31154721 (GRCh38) GRCh38 UCSC
8: 31012237 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.31012237C>G
LRG_524:g.126460C>G
LRG_524t1:c.3785C>G
... more HGVS
Protein change
T1262R
Other names
-
Canonical SPDI
NC_000008.11:31154720:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00311
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00346
1000 Genomes Project 0.00080
The Genome Aggregation Database (gnomAD) 0.00201
The Genome Aggregation Database (gnomAD), exomes 0.00273
Exome Aggregation Consortium (ExAC) 0.00274
Links
ClinGen: CA162758
dbSNP: rs78488552
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, single submitter Mar 8, 2017 RCV000122293.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 4, 2020 RCV000231281.10
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 20, 2021 RCV000858031.6
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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
(Mar 08, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229532.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (2)
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Werner syndrome
Allele origin: unknown
Mendelics
Accession: SCV001137603.1
Submitted: (Oct 22, 2019)
Evidence details
Uncertain significance
(Jun 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001155404.7
Submitted: (Jul 04, 2021)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Werner syndrome
Allele origin: germline
Invitae
Accession: SCV000285569.7
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Werner syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000473354.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Apr 20, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001795855.1
Submitted: (Aug 19, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 23891399, 26546047, 27153395, 24728327)
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000086520.1
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
Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. Maxwell KN American journal of human genetics 2016 PMID: 27153395
Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer. Smith AL Cancer letters 2016 PMID: 26546047
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://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=WRN - - - -

Text-mined citations for rs78488552...

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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