rs558813483
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_021098.3(CACNA1H):c.5974G>A(p.Gly1992Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,549,934 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 Likely benign (★★).
Frequency
Consequence
NM_021098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.5974G>A | p.Gly1992Ser | missense_variant | 34/35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.5956G>A | p.Gly1986Ser | missense_variant | 32/33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.5935G>A | p.Gly1979Ser | missense_variant | 34/35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000569107.5 | c.2212G>A | p.Gly738Ser | missense_variant | 16/17 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000564231.5 | c.2164G>A | p.Gly722Ser | missense_variant | 17/18 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000562079.5 | c.2146G>A | p.Gly716Ser | missense_variant | 16/17 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000639478.1 | n.*1022G>A | non_coding_transcript_exon_variant | 34/35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*3792G>A | non_coding_transcript_exon_variant | 34/35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000639478.1 | n.*1022G>A | 3_prime_UTR_variant | 34/35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*3792G>A | 3_prime_UTR_variant | 34/35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000592 AC: 9AN: 152012Hom.: 0 AF XY: 0.0000246 AC XY: 2AN XY: 81212
GnomAD4 exome AF: 0.0000179 AC: 25AN: 1397620Hom.: 0 Cov.: 34 AF XY: 0.0000145 AC XY: 10AN XY: 689362
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74478
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at