rs3764615
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001127222.2(CACNA1A):c.400-123G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 909,456 control chromosomes in the GnomAD database, including 6,238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001127222.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.400-123G>T | intron_variant | Intron 2 of 46 | 1 | NM_001127222.2 | ENSP00000353362.5 | |||
CACNA1A | ENST00000638029.1 | c.400-123G>T | intron_variant | Intron 2 of 47 | 5 | ENSP00000489829.1 | ||||
CACNA1A | ENST00000573710.7 | c.400-123G>T | intron_variant | Intron 2 of 46 | 5 | ENSP00000460092.3 | ||||
CACNA1A | ENST00000635727.1 | c.400-123G>T | intron_variant | Intron 2 of 46 | 5 | ENSP00000490001.1 | ||||
CACNA1A | ENST00000637769.1 | c.400-123G>T | intron_variant | Intron 2 of 46 | 1 | ENSP00000489778.1 | ||||
CACNA1A | ENST00000636012.1 | c.400-123G>T | intron_variant | Intron 2 of 45 | 5 | ENSP00000490223.1 | ||||
CACNA1A | ENST00000637736.1 | c.259-123G>T | intron_variant | Intron 1 of 45 | 5 | ENSP00000489861.1 | ||||
CACNA1A | ENST00000636389.1 | c.400-123G>T | intron_variant | Intron 2 of 46 | 5 | ENSP00000489992.1 | ||||
CACNA1A | ENST00000637432.1 | c.400-123G>T | intron_variant | Intron 2 of 47 | 5 | ENSP00000490617.1 | ||||
CACNA1A | ENST00000636549.1 | c.400-123G>T | intron_variant | Intron 2 of 47 | 5 | ENSP00000490578.1 | ||||
CACNA1A | ENST00000637927.1 | c.400-123G>T | intron_variant | Intron 2 of 46 | 5 | ENSP00000489715.1 | ||||
CACNA1A | ENST00000635895.1 | c.400-123G>T | intron_variant | Intron 2 of 46 | 5 | ENSP00000490323.1 | ||||
CACNA1A | ENST00000638009.2 | c.400-123G>T | intron_variant | Intron 2 of 46 | 1 | ENSP00000489913.1 | ||||
CACNA1A | ENST00000637276.1 | c.400-123G>T | intron_variant | Intron 2 of 45 | 5 | ENSP00000489777.1 |
Frequencies
GnomAD3 genomes AF: 0.126 AC: 19175AN: 151986Hom.: 1535 Cov.: 32
GnomAD4 exome AF: 0.0967 AC: 73233AN: 757352Hom.: 4699 AF XY: 0.0985 AC XY: 38456AN XY: 390552
GnomAD4 genome AF: 0.126 AC: 19205AN: 152104Hom.: 1539 Cov.: 32 AF XY: 0.130 AC XY: 9670AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:2
- -
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at