rs58124832
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_021098.3(CACNA1H):c.5612G>A(p.Arg1871Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 1,561,046 control chromosomes in the GnomAD database, including 3,036 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1871W) has been classified as Uncertain significance.
Frequency
Consequence
NM_021098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1H | NM_021098.3 | c.5612G>A | p.Arg1871Gln | missense_variant | 33/35 | ENST00000348261.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.5612G>A | p.Arg1871Gln | missense_variant | 33/35 | 1 | NM_021098.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0451 AC: 6863AN: 152190Hom.: 229 Cov.: 34
GnomAD3 exomes AF: 0.0548 AC: 9431AN: 172182Hom.: 337 AF XY: 0.0588 AC XY: 5378AN XY: 91508
GnomAD4 exome AF: 0.0586 AC: 82512AN: 1408738Hom.: 2806 Cov.: 33 AF XY: 0.0597 AC XY: 41527AN XY: 695890
GnomAD4 genome ? AF: 0.0451 AC: 6865AN: 152308Hom.: 230 Cov.: 34 AF XY: 0.0438 AC XY: 3259AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 22, 2019 | This variant is associated with the following publications: (PMID: 28933792) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at