1-34784745-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_024009.3(GJB3):c.-18C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,598,814 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_024009.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJB3 | NM_024009.3 | c.-18C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 2 | ENST00000373366.3 | NP_076872.1 | ||
GJB3 | NM_024009.3 | c.-18C>T | 5_prime_UTR_variant | Exon 2 of 2 | ENST00000373366.3 | NP_076872.1 | ||
GJB3 | NM_001005752.2 | c.-18C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 2 | NP_001005752.1 | |||
GJB3 | NM_001005752.2 | c.-18C>T | 5_prime_UTR_variant | Exon 2 of 2 | NP_001005752.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJB3 | ENST00000373366 | c.-18C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 2 | 1 | NM_024009.3 | ENSP00000362464.2 | |||
GJB3 | ENST00000373366 | c.-18C>T | 5_prime_UTR_variant | Exon 2 of 2 | 1 | NM_024009.3 | ENSP00000362464.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248934Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134626
GnomAD4 exome AF: 0.0000270 AC: 39AN: 1446628Hom.: 0 Cov.: 31 AF XY: 0.0000222 AC XY: 16AN XY: 720324
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
Erythrokeratodermia variabilis et progressiva 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at