chr8-106692797-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001198533.2(OXR1):āc.595G>Cā(p.Val199Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000499 in 1,603,930 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 Uncertain significance (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 31)
Exomes š: 0.0000034 ( 0 hom. )
Consequence
OXR1
NM_001198533.2 missense
NM_001198533.2 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 7.77
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 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3375841).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 150820Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249994Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135218
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GnomAD4 exome AF: 0.00000344 AC: 5AN: 1453110Hom.: 0 Cov.: 27 AF XY: 0.00000553 AC XY: 4AN XY: 723410
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GnomAD4 genome AF: 0.0000199 AC: 3AN: 150820Hom.: 0 Cov.: 31 AF XY: 0.0000272 AC XY: 2AN XY: 73462
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.598G>C (p.V200L) alteration is located in exon 6 (coding exon 6) of the OXR1 gene. This alteration results from a G to C substitution at nucleotide position 598, causing the valine (V) at amino acid position 200 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
D;.;D;D;D
Vest4
MutPred
0.20
.;.;Gain of sheet (P = 0.039);.;.;
MVP
MPC
0.28
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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