rs370348070
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001127222.2(CACNA1A):c.4591-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000636 in 1,586,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001127222.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.4591-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000360228.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.4591-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001127222.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152092Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000684 AC: 16AN: 233872Hom.: 0 AF XY: 0.0000790 AC XY: 10AN XY: 126580
GnomAD4 exome AF: 0.0000669 AC: 96AN: 1434806Hom.: 0 Cov.: 31 AF XY: 0.0000677 AC XY: 48AN XY: 708692
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152092Hom.: 0 Cov.: 30 AF XY: 0.0000538 AC XY: 4AN XY: 74298
ClinVar
Submissions by phenotype
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 29, 2020 | - - |
CACNA1A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 03, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at