chr3-105867592-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_170662.5(CBLB):c.-14-1G>T variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,613,662 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
NM_170662.5 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBLB | NM_170662.5 | c.-14-1G>T | splice_acceptor_variant, intron_variant | ENST00000394030.8 | NP_733762.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CBLB | ENST00000394030.8 | c.-14-1G>T | splice_acceptor_variant, intron_variant | 1 | NM_170662.5 | ENSP00000377598.4 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000347 AC: 87AN: 250618Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135586
GnomAD4 exome AF: 0.000109 AC: 159AN: 1461444Hom.: 2 Cov.: 31 AF XY: 0.000110 AC XY: 80AN XY: 727056
GnomAD4 genome AF: 0.000125 AC: 19AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74414
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at