1-201073607-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_000069.3(CACNA1S):c.2099C>T(p.Thr700Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00023 in 1,614,156 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T700T) has been classified as Likely benign.
Frequency
Consequence
NM_000069.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251488Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135920
GnomAD4 exome AF: 0.000238 AC: 348AN: 1461850Hom.: 1 Cov.: 32 AF XY: 0.000237 AC XY: 172AN XY: 727236
GnomAD4 genome AF: 0.000151 AC: 23AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74486
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Reported previously in an individual with susceptibility to malignant hyperthermia who also harbored another CACNA1S variant, as well as a variant in RYR1 (PMID: 25735680); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25735680) -
CACNA1S: BP4 -
CACNA1S-related disorder Uncertain:1
The CACNA1S c.2099C>T variant is predicted to result in the amino acid substitution p.Thr700Met. This variant was observed along with a second CACNA1S variant in an individual undergoing testing for malignant hyperthermia (Gillies et al. 2015. PubMed ID: 25735680). This variant is reported in 0.037% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Malignant hyperthermia, susceptibility to, 5 Uncertain:1
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not specified Benign:1
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Malignant hyperthermia, susceptibility to, 5;C2749982:Thyrotoxic periodic paralysis, susceptibility to, 1;C3714580:Hypokalemic periodic paralysis, type 1;C5830283:Congenital myopathy 18 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