16-1220167-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021098.3(CACNA1H):c.6235G>C(p.Val2079Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2079I) has been classified as Likely benign.
Frequency
Consequence
NM_021098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.6235G>C | p.Val2079Leu | missense_variant | Exon 35 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.6217G>C | p.Val2073Leu | missense_variant | Exon 33 of 33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.6196G>C | p.Val2066Leu | missense_variant | Exon 35 of 35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000569107.5 | c.2473G>C | p.Val825Leu | missense_variant | Exon 17 of 17 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000564231.5 | c.2425G>C | p.Val809Leu | missense_variant | Exon 18 of 18 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000562079.5 | c.2407G>C | p.Val803Leu | missense_variant | Exon 17 of 17 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000639478.1 | n.*1283G>C | non_coding_transcript_exon_variant | Exon 35 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*4053G>C | non_coding_transcript_exon_variant | Exon 35 of 35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000639478.1 | n.*1283G>C | 3_prime_UTR_variant | Exon 35 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*4053G>C | 3_prime_UTR_variant | Exon 35 of 35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 35
GnomAD4 exome Cov.: 73
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
Epilepsy, childhood absence, susceptibility to, 6;C4310756:Hyperaldosteronism, familial, type IV Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at