chr1-201039955-AGTAGCTCT-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PVS1_ModerateBP6_Very_StrongBS1BS2
The NM_000069.3(CACNA1S):c.5490_5497delAGAGCTAC(p.Leu1832ArgfsTer67) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,614,182 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000069.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CACNA1S | NM_000069.3 | c.5490_5497delAGAGCTAC | p.Leu1832ArgfsTer67 | frameshift_variant | Exon 44 of 44 | ENST00000362061.4 | NP_000060.2 | |
CACNA1S | XM_005245478.4 | c.5433_5440delAGAGCTAC | p.Leu1813ArgfsTer67 | frameshift_variant | Exon 43 of 43 | XP_005245535.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00557 AC: 848AN: 152196Hom.: 10 Cov.: 34
GnomAD3 exomes AF: 0.00126 AC: 316AN: 251410Hom.: 2 AF XY: 0.000949 AC XY: 129AN XY: 135878
GnomAD4 exome AF: 0.000545 AC: 797AN: 1461868Hom.: 5 AF XY: 0.000484 AC XY: 352AN XY: 727236
GnomAD4 genome AF: 0.00561 AC: 855AN: 152314Hom.: 10 Cov.: 34 AF XY: 0.00534 AC XY: 398AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:3
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. -
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Hypokalemic periodic paralysis, type 1 Benign:1
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Congenital myopathy 18 Benign:1
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Thyrotoxic periodic paralysis, susceptibility to, 1 Benign:1
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Malignant hyperthermia, susceptibility to, 5;C3714580:Hypokalemic periodic paralysis, type 1 Benign:1
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Malignant hyperthermia, susceptibility to, 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at