chr1-34785261-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM1BP4_StrongBP6BS1BS2_Supporting
The NM_024009.3(GJB3):c.499G>A(p.Val167Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,613,752 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024009.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJB3 | NM_024009.3 | c.499G>A | p.Val167Met | missense_variant | 2/2 | ENST00000373366.3 | NP_076872.1 | |
GJB3 | NM_001005752.2 | c.499G>A | p.Val167Met | missense_variant | 2/2 | NP_001005752.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJB3 | ENST00000373366.3 | c.499G>A | p.Val167Met | missense_variant | 2/2 | 1 | NM_024009.3 | ENSP00000362464 | P1 | |
GJB3 | ENST00000373362.3 | c.499G>A | p.Val167Met | missense_variant | 2/2 | 1 | ENSP00000362460 | P1 | ||
SMIM12 | ENST00000426886.1 | c.208-66852C>T | intron_variant, NMD_transcript_variant | 1 | ENSP00000429902 | |||||
ENST00000542839.1 | n.110+2727C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251328Hom.: 1 AF XY: 0.000339 AC XY: 46AN XY: 135860
GnomAD4 exome AF: 0.000156 AC: 228AN: 1461634Hom.: 1 Cov.: 33 AF XY: 0.000201 AC XY: 146AN XY: 727124
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 08, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 11, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 04, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 25, 2020 | - - |
Autosomal recessive nonsyndromic hearing loss 1A;C2675236:Autosomal dominant nonsyndromic hearing loss 2B;C4551486:Erythrokeratodermia variabilis et progressiva 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at