rs563361414
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000348261.11(CACNA1H):c.5445+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000557 in 1,596,614 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000348261.11 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1H | NM_021098.3 | c.5445+7G>A | splice_region_variant, intron_variant | ENST00000348261.11 | NP_066921.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.5445+7G>A | splice_region_variant, intron_variant | 1 | NM_021098.3 | ENSP00000334198 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00127 AC: 285AN: 224150Hom.: 1 AF XY: 0.00169 AC XY: 206AN XY: 121974
GnomAD4 exome AF: 0.000586 AC: 846AN: 1444266Hom.: 8 Cov.: 32 AF XY: 0.000853 AC XY: 611AN XY: 716366
GnomAD4 genome AF: 0.000289 AC: 44AN: 152348Hom.: 0 Cov.: 34 AF XY: 0.000389 AC XY: 29AN XY: 74490
ClinVar
Submissions by phenotype
CACNA1H-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at