1-201039852-GGTCTCC-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_000069.3(CACNA1S):c.5595_5600delGGAGAC(p.Gln1865_Thr1867delinsHis) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000412 in 1,455,000 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000069.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1S | NM_000069.3 | c.5595_5600delGGAGAC | p.Gln1865_Thr1867delinsHis | disruptive_inframe_deletion | Exon 44 of 44 | ENST00000362061.4 | NP_000060.2 | |
CACNA1S | XM_005245478.4 | c.5538_5543delGGAGAC | p.Gln1846_Thr1848delinsHis | disruptive_inframe_deletion | Exon 43 of 43 | XP_005245535.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246464Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133630
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455000Hom.: 0 AF XY: 0.00000276 AC XY: 2AN XY: 724148
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Malignant hyperthermia, susceptibility to, 5;C3714580:Hypokalemic periodic paralysis, type 1 Uncertain:1
This variant has not been reported in the literature in individuals affected with CACNA1S-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant, c.5595_5600del, is a complex sequence change that results in the deletion of 3 and insertion of 1 amino acid(s) in the CACNA1S protein (p.Gln1865_Thr1867delinsHis). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at