16-1200511-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_021098.3(CACNA1H):c.1059C>T(p.Asn353Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000201 in 1,612,324 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021098.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.1059C>T | p.Asn353Asn | synonymous_variant | Exon 7 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.1059C>T | p.Asn353Asn | synonymous_variant | Exon 6 of 33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.1020C>T | p.Asn340Asn | synonymous_variant | Exon 7 of 35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000639478.1 | n.1059C>T | non_coding_transcript_exon_variant | Exon 7 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.1059C>T | non_coding_transcript_exon_variant | Exon 7 of 35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.00107 AC: 163AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000223 AC: 55AN: 246976Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134562
GnomAD4 exome AF: 0.000108 AC: 158AN: 1459998Hom.: 1 Cov.: 34 AF XY: 0.0000964 AC XY: 70AN XY: 726286
GnomAD4 genome AF: 0.00109 AC: 166AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.00113 AC XY: 84AN XY: 74478
ClinVar
Submissions by phenotype
Epilepsy, childhood absence, susceptibility to, 6;C4310756:Hyperaldosteronism, familial, type IV Benign:1
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CACNA1H-related disorder Benign:1
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
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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