12-48824661-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000725.4(CACNB3):c.408-8C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00173 in 1,612,758 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000725.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNB3 | NM_000725.4 | c.408-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000301050.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNB3 | ENST00000301050.7 | c.408-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000725.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00951 AC: 1445AN: 151994Hom.: 31 Cov.: 30
GnomAD3 exomes AF: 0.00256 AC: 641AN: 250814Hom.: 14 AF XY: 0.00168 AC XY: 228AN XY: 135674
GnomAD4 exome AF: 0.000919 AC: 1343AN: 1460646Hom.: 21 Cov.: 32 AF XY: 0.000802 AC XY: 583AN XY: 726644
GnomAD4 genome AF: 0.00953 AC: 1450AN: 152112Hom.: 31 Cov.: 30 AF XY: 0.00888 AC XY: 660AN XY: 74362
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at