rs368553931
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_021098.3(CACNA1H):c.6014G>A(p.Arg2005His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000899 in 1,546,728 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 Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2005C) has been classified as Benign.
Frequency
Consequence
NM_021098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.6014G>A | p.Arg2005His | missense_variant | 34/35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.5996G>A | p.Arg1999His | missense_variant | 32/33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.5975G>A | p.Arg1992His | missense_variant | 34/35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000569107.5 | c.2252G>A | p.Arg751His | missense_variant | 16/17 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000564231.5 | c.2204G>A | p.Arg735His | missense_variant | 17/18 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000562079.5 | c.2186G>A | p.Arg729His | missense_variant | 16/17 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000639478.1 | n.*1062G>A | non_coding_transcript_exon_variant | 34/35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*3832G>A | non_coding_transcript_exon_variant | 34/35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000639478.1 | n.*1062G>A | 3_prime_UTR_variant | 34/35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*3832G>A | 3_prime_UTR_variant | 34/35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000201 AC: 3AN: 149062Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 79670
GnomAD4 exome AF: 0.0000947 AC: 132AN: 1394540Hom.: 0 Cov.: 34 AF XY: 0.0000931 AC XY: 64AN XY: 687474
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at