rs202115678
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_021098.3(CACNA1H):c.3970-5G>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 0.00012 in 1,609,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_021098.3 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- hyperaldosteronism, familial, type IVInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- childhood absence epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- epilepsy, childhood absence, susceptibility to, 6Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | 1 | NM_021098.3 | ENSP00000334198.7 | |||
CACNA1H | ENST00000569107.6 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | 1 | ENSP00000454990.2 | ||||
CACNA1H | ENST00000711493.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | ENSP00000518778.1 | |||||
CACNA1H | ENST00000565831.7 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | 1 | ENSP00000455840.1 | ||||
CACNA1H | ENST00000711450.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | ENSP00000518762.1 | |||||
CACNA1H | ENST00000564231.6 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | 1 | ENSP00000457555.2 | ||||
CACNA1H | ENST00000638323.1 | c.3931-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | 5 | ENSP00000492267.1 | ||||
CACNA1H | ENST00000562079.6 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | 1 | ENSP00000454581.2 | ||||
CACNA1H | ENST00000711438.1 | c.3931-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | ENSP00000518754.1 | |||||
CACNA1H | ENST00000711482.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518771.1 | |||||
CACNA1H | ENST00000711485.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | ENSP00000518774.1 | |||||
CACNA1H | ENST00000711455.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518768.1 | |||||
CACNA1H | ENST00000711483.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | ENSP00000518772.1 | |||||
CACNA1H | ENST00000711456.1 | c.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | ENSP00000518769.1 | |||||
CACNA1H | ENST00000621827.2 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 36 | 6 | ENSP00000518766.1 | ||||
CACNA1H | ENST00000637236.3 | n.4020-5G>A | splice_region_variant, intron_variant | Intron 19 of 33 | 5 | ENSP00000492650.2 | ||||
CACNA1H | ENST00000639478.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*1883-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000711442.1 | n.*3417-5G>A | splice_region_variant, intron_variant | Intron 18 of 33 | ENSP00000518758.1 | |||||
CACNA1H | ENST00000711448.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518760.1 | |||||
CACNA1H | ENST00000711449.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | ENSP00000518761.1 | |||||
CACNA1H | ENST00000711451.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518763.1 | |||||
CACNA1H | ENST00000711452.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518764.1 | |||||
CACNA1H | ENST00000711453.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518765.1 | |||||
CACNA1H | ENST00000711484.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | ENSP00000518773.1 | |||||
CACNA1H | ENST00000711486.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 36 | ENSP00000518775.1 | |||||
CACNA1H | ENST00000711487.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 35 | ENSP00000518776.1 | |||||
CACNA1H | ENST00000711488.1 | n.3970-5G>A | splice_region_variant, intron_variant | Intron 19 of 34 | ENSP00000518777.1 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152136Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000253 AC: 62AN: 244720 AF XY: 0.000299 show subpopulations
GnomAD4 exome AF: 0.0000968 AC: 141AN: 1457014Hom.: 0 Cov.: 40 AF XY: 0.0000993 AC XY: 72AN XY: 724898 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000342 AC: 52AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74438 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at