9-137878041-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS2
The NM_000718.4(CACNA1B):c.108G>A(p.Gly36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000332 in 150,598 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 (★). Synonymous variant affecting the same amino acid position (i.e. G36G) has been classified as Likely benign.
Frequency
Consequence
NM_000718.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1B | NM_000718.4 | c.108G>A | p.Gly36= | synonymous_variant | 1/47 | ENST00000371372.6 | |
LOC100133077 | NR_121583.1 | n.2692-2361C>T | intron_variant, non_coding_transcript_variant | ||||
CACNA1B | NM_001243812.2 | c.108G>A | p.Gly36= | synonymous_variant | 1/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1B | ENST00000371372.6 | c.108G>A | p.Gly36= | synonymous_variant | 1/47 | 5 | NM_000718.4 | P4 | |
ENST00000371390.1 | n.2692-2361C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000332 AC: 5AN: 150598Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000368 AC: 4AN: 108714Hom.: 0 AF XY: 0.0000330 AC XY: 2AN XY: 60636
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000535 AC: 61AN: 1140226Hom.: 0 Cov.: 33 AF XY: 0.0000417 AC XY: 23AN XY: 550976
GnomAD4 genome ? AF: 0.0000332 AC: 5AN: 150598Hom.: 0 Cov.: 34 AF XY: 0.0000545 AC XY: 4AN XY: 73442
ClinVar
Submissions by phenotype
CACNA1B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2019 | 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