22-39570772-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_021096.4(CACNA1I):c.20C>T(p.Pro7Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00596 in 1,608,158 control chromosomes in the GnomAD database, including 494 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_021096.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1I | ENST00000402142.4 | c.20C>T | p.Pro7Leu | missense_variant | Exon 1 of 37 | 1 | NM_021096.4 | ENSP00000385019.3 | ||
CACNA1I | ENST00000404898.5 | c.20C>T | p.Pro7Leu | missense_variant | Exon 1 of 36 | 1 | ENSP00000384093.1 | |||
CACNA1I | ENST00000401624.5 | c.20C>T | p.Pro7Leu | missense_variant | Exon 1 of 36 | 1 | ENSP00000383887.1 | |||
CACNA1I | ENST00000407673.5 | c.20C>T | p.Pro7Leu | missense_variant | Exon 1 of 35 | 1 | ENSP00000385680.1 |
Frequencies
GnomAD3 genomes AF: 0.0309 AC: 4700AN: 152108Hom.: 262 Cov.: 31
GnomAD3 exomes AF: 0.00746 AC: 1745AN: 234048Hom.: 79 AF XY: 0.00602 AC XY: 771AN XY: 128026
GnomAD4 exome AF: 0.00334 AC: 4862AN: 1455932Hom.: 230 Cov.: 31 AF XY: 0.00294 AC XY: 2125AN XY: 724004
GnomAD4 genome AF: 0.0310 AC: 4720AN: 152226Hom.: 264 Cov.: 31 AF XY: 0.0295 AC XY: 2199AN XY: 74422
ClinVar
Submissions by phenotype
CACNA1I-related disorder Benign:1
This variant is classified as 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