rs200333359
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 1P and 11B. PP2BP4_ModerateBP6BS1BS2
The NM_001127222.2(CACNA1A):c.3410C>T(p.Pro1137Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000278 in 1,544,684 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1137R) has been classified as Likely benign.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.3410C>T | p.Pro1137Leu | missense_variant | 20/47 | ENST00000360228.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.3410C>T | p.Pro1137Leu | missense_variant | 20/47 | 1 | NM_001127222.2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151924Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000418 AC: 8AN: 191438Hom.: 0 AF XY: 0.0000294 AC XY: 3AN XY: 101924
GnomAD4 exome AF: 0.0000187 AC: 26AN: 1392642Hom.: 0 Cov.: 35 AF XY: 0.0000204 AC XY: 14AN XY: 685316
GnomAD4 genome AF: 0.000112 AC: 17AN: 152042Hom.: 0 Cov.: 30 AF XY: 0.000121 AC XY: 9AN XY: 74336
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | CACNA1A: PP2 - |
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at