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NM_000124.4(ERCC6):c.2096C>T (p.Thr699Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Oct 1, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000287219.9
Variation ID:
287219
Description:
single nucleotide variant
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NM_000124.4(ERCC6):c.2096C>T (p.Thr699Met)

Allele ID
271456
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q11.23
Genomic location
10: 49482760 (GRCh38) GRCh38 UCSC
10: 50690806 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_465:g.61342C>T
LRG_465t1:c.2096C>T
NC_000010.10:g.50690806G>A
... more HGVS
Protein change
T699M
Other names
-
Canonical SPDI
NC_000010.11:49482759:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (A)

Allele frequency
1000 Genomes Project 0.00180
The Genome Aggregation Database (gnomAD), exomes 0.00038
The Genome Aggregation Database (gnomAD) 0.00142
Trans-Omics for Precision Medicine (TOPMed) 0.00161
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00169
Exome Aggregation Consortium (ExAC) 0.00048
The Genome Aggregation Database (gnomAD) 0.00124
Trans-Omics for Precision Medicine (TOPMed) 0.00156
Links
ClinGen: CA5495770
dbSNP: rs55698015
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000263243.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000304579.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000358004.2
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Dec 4, 2020 RCV000725973.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ERCC6 - - GRCh38
GRCh37
531 825

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Cerebrooculofacioskeletal Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000362895.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Cockayne Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000362896.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Macular Degeneration
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000362894.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(May 13, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000340926.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001019864.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Sep 08, 2019)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories,Mayo Clinic
Accession: SCV001714948.1
Submitted: (May 26, 2021)
Evidence details
Uncertain significance
(Aug 21, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000590359.4
Submitted: (Oct 01, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our … (more)

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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ERCC6 - - - -

Text-mined citations for rs55698015...

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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 Dec 02, 2021