chr16-1204076-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_021098.3(CACNA1H):c.2069C>T(p.Ala690Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000493 in 1,604,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A690A) has been classified 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1H | NM_021098.3 | c.2069C>T | p.Ala690Val | missense_variant | 10/35 | ENST00000348261.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.2069C>T | p.Ala690Val | missense_variant | 10/35 | 1 | NM_021098.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000190 AC: 29AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000248 AC: 57AN: 230018Hom.: 0 AF XY: 0.000214 AC XY: 27AN XY: 126352
GnomAD4 exome AF: 0.000525 AC: 762AN: 1452330Hom.: 0 Cov.: 32 AF XY: 0.000518 AC XY: 374AN XY: 721634
GnomAD4 genome AF: 0.000190 AC: 29AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74500
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 08, 2018 | - - |
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at