rs41267497
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000069.3(CACNA1S):c.4860C>T(p.Pro1620Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,613,800 control chromosomes in the GnomAD database, including 18,382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000069.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.105 AC: 15883AN: 151930Hom.: 1167 Cov.: 31
GnomAD3 exomes AF: 0.105 AC: 26402AN: 251320Hom.: 1917 AF XY: 0.105 AC XY: 14250AN XY: 135842
GnomAD4 exome AF: 0.144 AC: 210454AN: 1461752Hom.: 17216 Cov.: 33 AF XY: 0.140 AC XY: 102151AN XY: 727178
GnomAD4 genome AF: 0.104 AC: 15880AN: 152048Hom.: 1166 Cov.: 31 AF XY: 0.101 AC XY: 7472AN XY: 74298
ClinVar
Submissions by phenotype
not specified Benign:4
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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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Malignant hyperthermia, susceptibility to, 5 Benign:3
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Hypokalemic periodic paralysis, type 1 Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Congenital myopathy 18 Benign:1
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Thyrotoxic periodic paralysis, susceptibility to, 1 Benign:1
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not provided Benign:1
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Malignant hyperthermia, susceptibility to, 5;C3714580:Hypokalemic periodic paralysis, type 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at