chr1-201069559-A-G
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_000069.3(CACNA1S):āc.2403T>Cā(p.Phe801Phe) variant causes a synonymous change. The variant allele was found at a frequency of 0.419 in 1,570,430 control chromosomes in the GnomAD database, including 147,909 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000069.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.421 AC: 63950AN: 151872Hom.: 14602 Cov.: 32
GnomAD3 exomes AF: 0.333 AC: 59753AN: 179650Hom.: 11942 AF XY: 0.329 AC XY: 31199AN XY: 94918
GnomAD4 exome AF: 0.419 AC: 593924AN: 1418440Hom.: 133302 Cov.: 42 AF XY: 0.411 AC XY: 288123AN XY: 700866
GnomAD4 genome AF: 0.421 AC: 63985AN: 151990Hom.: 14607 Cov.: 32 AF XY: 0.405 AC XY: 30078AN XY: 74314
ClinVar
Submissions by phenotype
not specified Benign:5
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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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Hypokalemic periodic paralysis, type 1 Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
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not provided Benign:2
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Malignant hyperthermia, susceptibility to, 5 Benign:2
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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