rs72552061
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021098.3(CACNA1H):c.4778-5C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,395,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_021098.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1H | NM_021098.3 | c.4778-5C>A | splice_region_variant, intron_variant | ENST00000348261.11 | NP_066921.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.4778-5C>A | splice_region_variant, intron_variant | 1 | NM_021098.3 | ENSP00000334198.7 | ||||
CACNA1H | ENST00000565831.6 | c.4760-5C>A | splice_region_variant, intron_variant | 1 | ENSP00000455840.1 | |||||
CACNA1H | ENST00000638323.1 | c.4739-5C>A | splice_region_variant, intron_variant | 5 | ENSP00000492267.1 | |||||
CACNA1H | ENST00000569107.5 | c.1016-5C>A | splice_region_variant, intron_variant | 1 | ENSP00000454990.2 | |||||
CACNA1H | ENST00000564231.5 | c.1001-5C>A | splice_region_variant, intron_variant | 1 | ENSP00000457555.2 | |||||
CACNA1H | ENST00000562079.5 | c.983-5C>A | splice_region_variant, intron_variant | 1 | ENSP00000454581.2 | |||||
CACNA1H | ENST00000639478.1 | n.4716-5C>A | splice_region_variant, intron_variant | 5 | ENSP00000491945.1 | |||||
CACNA1H | ENST00000640028.1 | n.*2629-5C>A | splice_region_variant, intron_variant | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 155958Hom.: 0 AF XY: 0.0000119 AC XY: 1AN XY: 83750
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1395590Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 688868
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at