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NM_000719.7(CACNA1C):c.5214C>A (p.Gly1738=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 30, 2021)
Last evaluated:
Jun 1, 2021
Accession:
VCV000136632.9
Variation ID:
136632
Description:
single nucleotide variant
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NM_000719.7(CACNA1C):c.5214C>A (p.Gly1738=)

Allele ID
140335
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12p13.33
Genomic location
12: 2679566 (GRCh38) GRCh38 UCSC
12: 2788732 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_334:g.713781C>A
LRG_334t1:c.5214C>A
NC_000012.11:g.2788732C>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000012.12:2679565:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00133
Trans-Omics for Precision Medicine (TOPMed) 0.00110
1000 Genomes Project 0.00100
Links
ClinGen: CA232435
dbSNP: rs199538058
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 Dec 23, 2014 RCV000225692.4
Likely benign 1 criteria provided, single submitter Nov 27, 2015 RCV000249460.1
Likely benign 1 criteria provided, single submitter Nov 27, 2015 RCV000716788.1
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV001086120.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jun 1, 2021 RCV000724269.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CACNA1C Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1101 1653
CACNA1C-AS1 - - - GRCh38
GRCh38
- 477

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 23, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167501.9
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)
Uncertain significance
(May 15, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230571.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Nov 27, 2015)
criteria provided, single submitter
Method: clinical testing
cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000318392.4
Submitted: (Jul 30, 2018)
Evidence details
Comment:
Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign,Subpopulation frequency in support of benign classification
Likely benign
(Nov 27, 2015)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000847631.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Subpopulation frequency in support of benign classification;Synonymous alterations with insufficient evidence to classify as benign
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome
Allele origin: germline
Invitae
Accession: SCV000285593.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001747643.1
Submitted: (Jul 04, 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: SCV001922565.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001958570.1
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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CACNA1C - - - -

Text-mined citations for rs199538058...

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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 30, 2021