10-18539517-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_201596.3(CACNB2):c.1776C>T(p.Asp592Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,820 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_201596.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNB2 | ENST00000324631.13 | c.1776C>T | p.Asp592Asp | synonymous_variant | Exon 14 of 14 | 1 | NM_201596.3 | ENSP00000320025.8 | ||
CACNB2 | ENST00000377329.10 | c.1614C>T | p.Asp538Asp | synonymous_variant | Exon 13 of 13 | 1 | NM_201590.3 | ENSP00000366546.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151968Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251314Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135828
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461852Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727226
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151968Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74226
ClinVar
Submissions by phenotype
Brugada syndrome 4 Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at