chrX-71223169-AAAGG-CAAGT
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The ENST00000675609.1(GJB1):c.-165-18_-165-14delinsCAAGT variant causes a splice polypyrimidine tract, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 22)
Consequence
GJB1
ENST00000675609.1 splice_polypyrimidine_tract, intron
ENST00000675609.1 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.79
Genes affected
GJB1 (HGNC:4283): (gap junction protein beta 1) This gene encodes a member of the gap junction protein family. The gap junction proteins are membrane-spanning proteins that assemble to form gap junction channels that facilitate the transfer of ions and small molecules between cells. According to sequence similarities at the nucleotide and amino acid levels, the gap junction proteins are divided into two categories, alpha and beta. Mutations in this gene cause X-linked Charcot-Marie-Tooth disease, an inherited peripheral neuropathy. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJB1 | NM_001097642.3 | c.-16-523_-16-519delinsCAAGT | intron_variant | ||||
GJB1 | XM_011530907.3 | c.-17+403_-17+407delinsCAAGT | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJB1 | ENST00000374029.2 | c.-16-523_-16-519delinsCAAGT | intron_variant | 5 | P1 | ||||
GJB1 | ENST00000447581.2 | c.-17+403_-17+407delinsCAAGT | intron_variant | 5 | P1 | ||||
GJB1 | ENST00000645009.2 | c.-16-523_-16-519delinsCAAGT | intron_variant | P1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2017 | The c.-183_-179delAAAGGinsCAAGT variant has not been published as a pathogenic variant, nor hasit been reported as a benign variant to our knowledge. No data are available from control populationsto assess the frequency of this variant. The c.-183_-179delAAAGGinsCAAGT variant may affect a 5'regulatory region; however, in the absence of RNA/functional studies, the actual effect of this sequencechange in this individual is unknown. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at