chr8-106692712-TAAA-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001198533.2(OXR1):c.526-4_526-2del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,165,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000072 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00023 ( 0 hom. )
Consequence
OXR1
NM_001198533.2 splice_polypyrimidine_tract, intron
NM_001198533.2 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.226
Genes affected
OXR1 (HGNC:15822): (oxidation resistance 1) Predicted to enable oxidoreductase activity. Predicted to be involved in response to oxidative stress. Predicted to act upstream of or within several processes, including adult walking behavior; negative regulation of neuron death; and negative regulation of peptidyl-cysteine S-nitrosylation. Predicted to be located in mitochondrion and nucleolus. Predicted to be active in nucleus. Implicated in cerebellar hyplasia/atrophy, epilepsy, and global developmental delay. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
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Variant 8-106692712-TAAA-T is Benign according to our data. Variant chr8-106692712-TAAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 3044824.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OXR1 | NM_001198533.2 | c.526-4_526-2del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000517566.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXR1 | ENST00000517566.7 | c.526-4_526-2del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001198533.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000717 AC: 1AN: 139488Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000425 AC: 32AN: 75268Hom.: 0 AF XY: 0.000480 AC XY: 20AN XY: 41684
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GnomAD4 exome AF: 0.000230 AC: 236AN: 1025996Hom.: 0 AF XY: 0.000222 AC XY: 112AN XY: 503446
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GnomAD4 genome ? AF: 0.00000717 AC: 1AN: 139488Hom.: 0 Cov.: 30 AF XY: 0.0000148 AC XY: 1AN XY: 67564
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
OXR1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 22, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at