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NM_001127222.2(CACNA1A):c.3237C>T (p.Ala1079=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 23, 2021)
Last evaluated:
Nov 21, 2020
Accession:
VCV000128552.10
Variation ID:
128552
Description:
single nucleotide variant
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NM_001127222.2(CACNA1A):c.3237C>T (p.Ala1079=)

Allele ID
134001
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 13286819 (GRCh38) GRCh38 UCSC
19: 13397633 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_7:g.224642C>T
LRG_7t1:c.3240C>T LRG_7p1:p.Ala1080=
NC_000019.10:g.13286819G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:13286818:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00579 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00616
The Genome Aggregation Database (gnomAD), exomes 0.00136
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00553
The Genome Aggregation Database (gnomAD) 0.00594
Trans-Omics for Precision Medicine (TOPMed) 0.00602
Exome Aggregation Consortium (ExAC) 0.00170
1000 Genomes Project 0.00579
Trans-Omics for Precision Medicine (TOPMed) 0.00625
Links
ClinGen: CA152103
dbSNP: rs16026
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 Oct 20, 2016 RCV000116524.9
Benign 1 criteria provided, single submitter Oct 23, 2018 RCV000530595.5
Benign 1 criteria provided, single submitter Jun 27, 2016 RCV000718670.1
Benign 1 criteria provided, single submitter Nov 21, 2020 RCV001083730.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CACNA1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2001 2040

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 27, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000227639.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Oct 20, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000524680.4
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
(Oct 23, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143324.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Jun 27, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000849534.3
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
(Nov 21, 2020)
criteria provided, single submitter
Method: clinical testing
Developmental and epileptic encephalopathy, 42
Episodic ataxia type 2
Allele origin: germline
Invitae
Accession: SCV000656748.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000150473.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001932682.1
Submitted: (Sep 23, 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: SCV001968752.1
Submitted: (Sep 21, 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=CACNA1A - - - -

Text-mined citations for rs16026...

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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 Nov 27, 2021