9-137877927-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000718.4(CACNA1B):c.-7G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000135 in 148,022 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 (no stars).
Frequency
Consequence
NM_000718.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1B | ENST00000371372 | c.-7G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 47 | 5 | NM_000718.4 | ENSP00000360423.1 | |||
CACNA1B | ENST00000371363 | c.-7G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 46 | 5 | ENSP00000360414.1 | ||||
CACNA1B | ENST00000277551 | c.-7G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 47 | 5 | ENSP00000277551.2 | ||||
CACNA1B | ENST00000371372 | c.-7G>T | 5_prime_UTR_variant | Exon 1 of 47 | 5 | NM_000718.4 | ENSP00000360423.1 | |||
CACNA1B | ENST00000371363 | c.-7G>T | 5_prime_UTR_variant | Exon 1 of 46 | 5 | ENSP00000360414.1 | ||||
CACNA1B | ENST00000277551 | c.-7G>T | 5_prime_UTR_variant | Exon 1 of 47 | 5 | ENSP00000277551.2 | ||||
CACNA1B | ENST00000371357.5 | c.-7G>T | upstream_gene_variant | 5 | ENSP00000360408.1 |
Frequencies
GnomAD3 genomes AF: 0.0000135 AC: 2AN: 148022Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 899066Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 421306
GnomAD4 genome AF: 0.0000135 AC: 2AN: 148022Hom.: 0 Cov.: 33 AF XY: 0.0000139 AC XY: 1AN XY: 72070
ClinVar
Submissions by phenotype
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