rs16023
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001127222.2(CACNA1A):c.2975A>T(p.Glu992Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 1,502,488 control chromosomes in the GnomAD database, including 15,900 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E992Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
Publications
- episodic ataxia type 2Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- undetermined early-onset epileptic encephalopathyInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina
- developmental and epileptic encephalopathy, 42Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- migraine, familial hemiplegic, 1Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- spinocerebellar ataxia type 6Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
- benign paroxysmal torticollis of infancyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial or sporadic hemiplegic migraineInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Lennox-Gastaut syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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CACNA1A | ENST00000360228.11 | c.2975A>T | p.Glu992Val | missense_variant | Exon 19 of 47 | 1 | NM_001127222.2 | ENSP00000353362.5 | ||
CACNA1A | ENST00000638029.1 | c.2987A>T | p.Glu996Val | missense_variant | Exon 19 of 48 | 5 | ENSP00000489829.1 | |||
CACNA1A | ENST00000573710.7 | c.2981A>T | p.Glu994Val | missense_variant | Exon 19 of 47 | 5 | ENSP00000460092.3 | |||
CACNA1A | ENST00000635727.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 47 | 5 | ENSP00000490001.1 | |||
CACNA1A | ENST00000637769.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 47 | 1 | ENSP00000489778.1 | |||
CACNA1A | ENST00000636012.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 46 | 5 | ENSP00000490223.1 | |||
CACNA1A | ENST00000637736.1 | c.2837A>T | p.Glu946Val | missense_variant | Exon 18 of 46 | 5 | ENSP00000489861.1 | |||
CACNA1A | ENST00000636389.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 47 | 5 | ENSP00000489992.1 | |||
CACNA1A | ENST00000637432.1 | c.2987A>T | p.Glu996Val | missense_variant | Exon 19 of 48 | 5 | ENSP00000490617.1 | |||
CACNA1A | ENST00000636549.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 48 | 5 | ENSP00000490578.1 | |||
CACNA1A | ENST00000637927.1 | c.2981A>T | p.Glu994Val | missense_variant | Exon 19 of 47 | 5 | ENSP00000489715.1 | |||
CACNA1A | ENST00000635895.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 47 | 5 | ENSP00000490323.1 | |||
CACNA1A | ENST00000638009.2 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 47 | 1 | ENSP00000489913.1 | |||
CACNA1A | ENST00000637276.1 | c.2978A>T | p.Glu993Val | missense_variant | Exon 19 of 46 | 5 | ENSP00000489777.1 | |||
CACNA1A | ENST00000636768.2 | n.2978A>T | non_coding_transcript_exon_variant | Exon 19 of 45 | 5 | ENSP00000490190.2 | ||||
CACNA1A | ENST00000713789.1 | n.2975A>T | non_coding_transcript_exon_variant | Exon 19 of 47 | ENSP00000519091.1 |
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20277AN: 151782Hom.: 1410 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.137 AC: 14100AN: 102910 AF XY: 0.134 show subpopulations
GnomAD4 exome AF: 0.144 AC: 194404AN: 1350598Hom.: 14492 Cov.: 32 AF XY: 0.144 AC XY: 95757AN XY: 666138 show subpopulations
GnomAD4 genome AF: 0.133 AC: 20272AN: 151890Hom.: 1408 Cov.: 32 AF XY: 0.132 AC XY: 9802AN XY: 74268 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:10
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. -
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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. -
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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. -
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not provided Benign:1Other:1
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Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
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Inborn genetic diseases Benign:1
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