chr8-106679222-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001198533.2(OXR1):c.233A>G(p.Lys78Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000957 in 1,608,516 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000087 ( 0 hom. )
Consequence
OXR1
NM_001198533.2 missense
NM_001198533.2 missense
Scores
1
4
12
Clinical Significance
Conservation
PhyloP100: 8.69
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.013084382).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OXR1 | NM_001198533.2 | c.233A>G | p.Lys78Arg | missense_variant | 4/17 | ENST00000517566.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXR1 | ENST00000517566.7 | c.233A>G | p.Lys78Arg | missense_variant | 4/17 | 1 | NM_001198533.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152060Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000220 AC: 55AN: 249592Hom.: 0 AF XY: 0.000207 AC XY: 28AN XY: 135008
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GnomAD4 exome AF: 0.0000865 AC: 126AN: 1456338Hom.: 0 Cov.: 27 AF XY: 0.0000842 AC XY: 61AN XY: 724796
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GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74396
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3478
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hearing impairment Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Angen Gene Medicine Technology | - | - - |
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Mar 17, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
B;.;B;.;P;B
Vest4
MVP
MPC
0.21
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at