NM_000718.4:c.63C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_000718.4(CACNA1B):c.63C>T(p.Ala21Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000294 in 149,456 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1B | NM_000718.4 | c.63C>T | p.Ala21Ala | synonymous_variant | Exon 1 of 47 | ENST00000371372.6 | NP_000709.1 | |
CACNA1B | NM_001243812.2 | c.63C>T | p.Ala21Ala | synonymous_variant | Exon 1 of 47 | NP_001230741.1 | ||
LOC100133077 | NR_121583.1 | n.2692-2316G>A | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1B | ENST00000371372.6 | c.63C>T | p.Ala21Ala | synonymous_variant | Exon 1 of 47 | 5 | NM_000718.4 | ENSP00000360423.1 | ||
CACNA1B | ENST00000371357.5 | c.63C>T | p.Ala21Ala | synonymous_variant | Exon 1 of 46 | 5 | ENSP00000360408.1 | |||
CACNA1B | ENST00000371363.5 | c.63C>T | p.Ala21Ala | synonymous_variant | Exon 1 of 46 | 5 | ENSP00000360414.1 | |||
CACNA1B | ENST00000277551.6 | c.63C>T | p.Ala21Ala | synonymous_variant | Exon 1 of 47 | 5 | ENSP00000277551.2 |
Frequencies
GnomAD3 genomes AF: 0.000295 AC: 44AN: 149346Hom.: 0 Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000122 AC: 127AN: 1039834Hom.: 0 Cov.: 32 AF XY: 0.000156 AC XY: 77AN XY: 494224
GnomAD4 genome AF: 0.000294 AC: 44AN: 149456Hom.: 0 Cov.: 34 AF XY: 0.000493 AC XY: 36AN XY: 72958
ClinVar
Submissions by phenotype
not provided Benign:1
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