16-1204345-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_021098.3(CACNA1H):c.2338G>T(p.Val780Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,584,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021098.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1H | NM_021098.3 | c.2338G>T | p.Val780Phe | missense_variant | 10/35 | ENST00000348261.11 | NP_066921.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.2338G>T | p.Val780Phe | missense_variant | 10/35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.2338G>T | p.Val780Phe | missense_variant | 9/33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.2299G>T | p.Val767Phe | missense_variant | 10/35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000639478.1 | n.2338G>T | non_coding_transcript_exon_variant | 10/35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*251G>T | non_coding_transcript_exon_variant | 10/35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000640028.1 | n.*251G>T | 3_prime_UTR_variant | 10/35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000342 AC: 77AN: 225054Hom.: 0 AF XY: 0.000310 AC XY: 38AN XY: 122526
GnomAD4 exome AF: 0.000326 AC: 467AN: 1432562Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 220AN XY: 709212
GnomAD4 genome AF: 0.000315 AC: 48AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74384
ClinVar
Submissions by phenotype
CACNA1H-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 15, 2022 | 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
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at