9-137877951-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000718.4(CACNA1B):c.18C>T(p.Asp6Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00278 in 148,052 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000718.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1B | NM_000718.4 | c.18C>T | p.Asp6Asp | synonymous_variant | Exon 1 of 47 | ENST00000371372.6 | NP_000709.1 | |
CACNA1B | NM_001243812.2 | c.18C>T | p.Asp6Asp | synonymous_variant | Exon 1 of 47 | NP_001230741.1 | ||
LOC100133077 | NR_121583.1 | n.2692-2271G>A | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1B | ENST00000371372.6 | c.18C>T | p.Asp6Asp | synonymous_variant | Exon 1 of 47 | 5 | NM_000718.4 | ENSP00000360423.1 | ||
CACNA1B | ENST00000371357.5 | c.18C>T | p.Asp6Asp | synonymous_variant | Exon 1 of 46 | 5 | ENSP00000360408.1 | |||
CACNA1B | ENST00000371363.5 | c.18C>T | p.Asp6Asp | synonymous_variant | Exon 1 of 46 | 5 | ENSP00000360414.1 | |||
CACNA1B | ENST00000277551.6 | c.18C>T | p.Asp6Asp | synonymous_variant | Exon 1 of 47 | 5 | ENSP00000277551.2 |
Frequencies
GnomAD3 genomes AF: 0.00278 AC: 411AN: 147952Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00416 AC: 19AN: 4564Hom.: 0 AF XY: 0.00426 AC XY: 10AN XY: 2348
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00237 AC: 2201AN: 929218Hom.: 0 Cov.: 19 AF XY: 0.00236 AC XY: 1029AN XY: 436632
GnomAD4 genome AF: 0.00278 AC: 411AN: 148052Hom.: 1 Cov.: 33 AF XY: 0.00288 AC XY: 208AN XY: 72166
ClinVar
Submissions by phenotype
not provided Benign:3
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CACNA1B: BP4, BP7 -
CACNA1B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at