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NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 13, 2021)
Last evaluated:
May 3, 2021
Accession:
VCV000128551.9
Variation ID:
128551
Description:
single nucleotide variant
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NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)

Allele ID
134000
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 13298576 (GRCh38) GRCh38 UCSC
19: 13409390 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_7:g.212885G>A
NC_000019.10:g.13298576C>T
NC_000019.9:g.13409390C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:13298575:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.12380 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.12352
Exome Aggregation Consortium (ExAC) 0.14147
Trans-Omics for Precision Medicine (TOPMed) 0.14157
The Genome Aggregation Database (gnomAD), exomes 0.13266
The Genome Aggregation Database (gnomAD) 0.13724
1000 Genomes Project 0.12380
Links
ClinGen: CA152100
dbSNP: rs16025
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 6 criteria provided, multiple submitters, no conflicts May 3, 2021 RCV000116523.13
Benign 1 criteria provided, single submitter Mar 11, 2016 RCV000715030.1
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV001515627.1
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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
1886 1922

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000306695.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jan 08, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000518852.4
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
(May 03, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV000841259.3
Submitted: (Sep 13, 2021)
Evidence details
Benign
(Mar 18, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000202321.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 11, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000845853.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Epileptic encephalopathy, early infantile, 42
Episodic ataxia type 2
Allele origin: germline
Invitae
Accession: SCV001723739.1
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: SCV000150472.2
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
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001744040.3
Submitted: (Sep 02, 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 rs16025...

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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 Sep 18, 2021