1-34784692-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024009.3(GJB3):c.-25-46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00618 in 1,234,598 control chromosomes in the GnomAD database, including 306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024009.3 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJB3 | NM_024009.3 | c.-25-46A>G | intron_variant | Intron 1 of 1 | ENST00000373366.3 | NP_076872.1 | ||
GJB3 | NM_001005752.2 | c.-25-46A>G | intron_variant | Intron 1 of 1 | NP_001005752.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJB3 | ENST00000373366.3 | c.-25-46A>G | intron_variant | Intron 1 of 1 | 1 | NM_024009.3 | ENSP00000362464.2 | |||
GJB3 | ENST00000373362.3 | c.-25-46A>G | intron_variant | Intron 1 of 1 | 1 | ENSP00000362460.3 | ||||
SMIM12 | ENST00000426886.1 | n.208-66283T>C | intron_variant | Intron 2 of 4 | 1 | ENSP00000429902.1 | ||||
ENSG00000255811 | ENST00000542839.1 | n.110+3296T>C | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0259 AC: 3939AN: 152150Hom.: 162 Cov.: 32
GnomAD4 exome AF: 0.00340 AC: 3680AN: 1082330Hom.: 143 Cov.: 15 AF XY: 0.00294 AC XY: 1620AN XY: 550126
GnomAD4 genome AF: 0.0259 AC: 3945AN: 152268Hom.: 163 Cov.: 32 AF XY: 0.0253 AC XY: 1883AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:2
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at