rs200935259
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_000069.3(CACNA1S):c.4176C>G(p.Ser1392Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1392S) has been classified as Likely benign.
Frequency
Consequence
NM_000069.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251484Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727224
GnomAD4 genome AF: 0.000112 AC: 17AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74456
ClinVar
Submissions by phenotype
Malignant hyperthermia, susceptibility to, 5 Benign:2
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Malignant hyperthermia, susceptibility to, 5;C2749982:Thyrotoxic periodic paralysis, susceptibility to, 1;C3714580:Hypokalemic periodic paralysis, type 1 Benign:1
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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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at