rs112499125
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_024009.3(GJB3):c.33C>A(p.Ser11Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S11S) has been classified as Likely benign.
Frequency
Consequence
NM_024009.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJB3 | NM_024009.3 | c.33C>A | p.Ser11Arg | missense_variant | Exon 2 of 2 | ENST00000373366.3 | NP_076872.1 | |
GJB3 | NM_001005752.2 | c.33C>A | p.Ser11Arg | missense_variant | Exon 2 of 2 | NP_001005752.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJB3 | ENST00000373366.3 | c.33C>A | p.Ser11Arg | missense_variant | Exon 2 of 2 | 1 | NM_024009.3 | ENSP00000362464.2 | ||
GJB3 | ENST00000373362.3 | c.33C>A | p.Ser11Arg | missense_variant | Exon 2 of 2 | 1 | ENSP00000362460.3 | |||
SMIM12 | ENST00000426886.1 | n.208-66386G>T | intron_variant | Intron 2 of 4 | 1 | ENSP00000429902.1 | ||||
ENSG00000255811 | ENST00000542839.1 | n.110+3193G>T | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461850Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727216
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at