19-13207434-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_001127222.2(CACNA1A):c.7400G>A(p.Arg2467Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 1,519,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2467P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.7400G>A | p.Arg2467Gln | missense_variant | Exon 47 of 47 | 1 | NM_001127222.2 | ENSP00000353362.5 | ||
CACNA1A | ENST00000638029.1 | c.7418G>A | p.Arg2473Gln | missense_variant | Exon 48 of 48 | 5 | ENSP00000489829.1 | |||
CACNA1A | ENST00000573710.7 | c.7406G>A | p.Arg2469Gln | missense_variant | Exon 47 of 47 | 5 | ENSP00000460092.3 | |||
CACNA1A | ENST00000635727.1 | c.7403G>A | p.Arg2468Gln | missense_variant | Exon 47 of 47 | 5 | ENSP00000490001.1 | |||
CACNA1A | ENST00000637769.1 | c.7403G>A | p.Arg2468Gln | missense_variant | Exon 47 of 47 | 1 | ENSP00000489778.1 | |||
CACNA1A | ENST00000636012.1 | c.7367G>A | p.Arg2456Gln | missense_variant | Exon 46 of 46 | 5 | ENSP00000490223.1 | |||
CACNA1A | ENST00000637736.1 | c.7262G>A | p.Arg2421Gln | missense_variant | Exon 46 of 46 | 5 | ENSP00000489861.1 | |||
CACNA1A | ENST00000636389 | c.*486G>A | 3_prime_UTR_variant | Exon 47 of 47 | 5 | ENSP00000489992.1 | ||||
CACNA1A | ENST00000637432 | c.*612G>A | 3_prime_UTR_variant | Exon 48 of 48 | 5 | ENSP00000490617.1 | ||||
CACNA1A | ENST00000635895 | c.*612G>A | 3_prime_UTR_variant | Exon 47 of 47 | 5 | ENSP00000490323.1 | ||||
CACNA1A | ENST00000638009 | c.*612G>A | 3_prime_UTR_variant | Exon 47 of 47 | 1 | ENSP00000489913.1 | ||||
CACNA1A | ENST00000637276.1 | c.*612G>A | downstream_gene_variant | 5 | ENSP00000489777.1 |
Frequencies
GnomAD3 genomes AF: 0.0000463 AC: 7AN: 151318Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000158 AC: 2AN: 126668Hom.: 0 AF XY: 0.0000143 AC XY: 1AN XY: 70160
GnomAD4 exome AF: 0.0000168 AC: 23AN: 1368466Hom.: 0 Cov.: 30 AF XY: 0.0000163 AC XY: 11AN XY: 676518
GnomAD4 genome AF: 0.0000463 AC: 7AN: 151318Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 4AN XY: 73946
ClinVar
Submissions by phenotype
Episodic ataxia type 2 Uncertain:1
- -
not provided Uncertain:1
CACNA1A: PP2, PP3 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at