9-137878085-AGC-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_000718.4(CACNA1B):c.160_161delCG(p.Arg54AspfsTer66) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000718.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1B | NM_000718.4 | c.160_161delCG | p.Arg54AspfsTer66 | frameshift_variant | Exon 1 of 47 | ENST00000371372.6 | NP_000709.1 | |
CACNA1B | NM_001243812.2 | c.160_161delCG | p.Arg54AspfsTer66 | frameshift_variant | Exon 1 of 47 | NP_001230741.1 | ||
LOC100133077 | NR_121583.1 | n.2692-2407_2692-2406delGC | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1B | ENST00000371372.6 | c.160_161delCG | p.Arg54AspfsTer66 | frameshift_variant | Exon 1 of 47 | 5 | NM_000718.4 | ENSP00000360423.1 | ||
CACNA1B | ENST00000371357.5 | c.160_161delCG | p.Arg54AspfsTer66 | frameshift_variant | Exon 1 of 46 | 5 | ENSP00000360408.1 | |||
CACNA1B | ENST00000371363.5 | c.160_161delCG | p.Arg54AspfsTer66 | frameshift_variant | Exon 1 of 46 | 5 | ENSP00000360414.1 | |||
CACNA1B | ENST00000277551.6 | c.160_161delCG | p.Arg54AspfsTer66 | frameshift_variant | Exon 1 of 47 | 5 | ENSP00000277551.2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000252 AC: 3AN: 1190878Hom.: 0 AF XY: 0.00000345 AC XY: 2AN XY: 579460
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not provided Uncertain:1
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.