rs150245955
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024009.3(GJB3):c.313C>A(p.His105Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000364 in 1,614,088 control chromosomes in the GnomAD database, including 3 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 Likely benign (★★).
Frequency
Consequence
NM_024009.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJB3 | NM_024009.3 | c.313C>A | p.His105Asn | missense_variant | 2/2 | ENST00000373366.3 | |
GJB3 | NM_001005752.2 | c.313C>A | p.His105Asn | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJB3 | ENST00000373366.3 | c.313C>A | p.His105Asn | missense_variant | 2/2 | 1 | NM_024009.3 | P1 | |
GJB3 | ENST00000373362.3 | c.313C>A | p.His105Asn | missense_variant | 2/2 | 1 | P1 | ||
SMIM12 | ENST00000426886.1 | c.208-66666G>T | intron_variant, NMD_transcript_variant | 1 | |||||
ENST00000542839.1 | n.110+2913G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00212 AC: 323AN: 152168Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000562 AC: 141AN: 250876Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135592
GnomAD4 exome AF: 0.000181 AC: 265AN: 1461802Hom.: 0 Cov.: 33 AF XY: 0.000151 AC XY: 110AN XY: 727198
GnomAD4 genome AF: 0.00212 AC: 323AN: 152286Hom.: 3 Cov.: 32 AF XY: 0.00196 AC XY: 146AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 07, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | His105Asn in Exon 02 of GJB3: This variant is not expected to have clinical sign ificance because it has been identified in 0.6% (24/3738) of African American ch romosomes from a broad population by the NHLBI Exome Sequencing Project (http:// evs.gs.washington.edu/EVS; dbSNP rs150245955). - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 31, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
GJB3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 02, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at