rs16022
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001127222.2(CACNA1A):c.2751G>C(p.Glu917Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 1,592,562 control chromosomes in the GnomAD database, including 15,785 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. E917E) has been classified as Benign.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.2751G>C | p.Glu917Asp | missense_variant | 19/47 | ENST00000360228.11 | NP_001120694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.2751G>C | p.Glu917Asp | missense_variant | 19/47 | 1 | NM_001127222.2 | ENSP00000353362.5 | ||
CACNA1A | ENST00000638029.1 | c.2763G>C | p.Glu921Asp | missense_variant | 19/48 | 5 | ENSP00000489829.1 | |||
CACNA1A | ENST00000573710.7 | c.2757G>C | p.Glu919Asp | missense_variant | 19/47 | 5 | ENSP00000460092.3 | |||
CACNA1A | ENST00000635727.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/47 | 5 | ENSP00000490001.1 | |||
CACNA1A | ENST00000637769.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/47 | 1 | ENSP00000489778.1 | |||
CACNA1A | ENST00000636012.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/46 | 5 | ENSP00000490223.1 | |||
CACNA1A | ENST00000637736.1 | c.2613G>C | p.Glu871Asp | missense_variant | 18/46 | 5 | ENSP00000489861.1 | |||
CACNA1A | ENST00000636389.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/47 | 5 | ENSP00000489992.1 | |||
CACNA1A | ENST00000637432.1 | c.2763G>C | p.Glu921Asp | missense_variant | 19/48 | 5 | ENSP00000490617.1 | |||
CACNA1A | ENST00000636549.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/48 | 5 | ENSP00000490578.1 | |||
CACNA1A | ENST00000637927.1 | c.2757G>C | p.Glu919Asp | missense_variant | 19/47 | 5 | ENSP00000489715.1 | |||
CACNA1A | ENST00000635895.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/47 | 5 | ENSP00000490323.1 | |||
CACNA1A | ENST00000638009.2 | c.2754G>C | p.Glu918Asp | missense_variant | 19/47 | 1 | ENSP00000489913.1 | |||
CACNA1A | ENST00000637276.1 | c.2754G>C | p.Glu918Asp | missense_variant | 19/46 | 5 | ENSP00000489777.1 |
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18593AN: 152102Hom.: 1247 Cov.: 32
GnomAD3 exomes AF: 0.126 AC: 27267AN: 215748Hom.: 1777 AF XY: 0.125 AC XY: 15073AN XY: 120314
GnomAD4 exome AF: 0.140 AC: 201088AN: 1440352Hom.: 14538 Cov.: 33 AF XY: 0.139 AC XY: 99703AN XY: 716648
GnomAD4 genome AF: 0.122 AC: 18601AN: 152210Hom.: 1247 Cov.: 32 AF XY: 0.121 AC XY: 9005AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:9
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 03, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 30% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 28. Only high quality variants are reported. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 18, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | 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 disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 05, 2016 | 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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1Other:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at