chr8-106686738-A-G

Position:

• chr8-106686738-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198533.2(OXR1):​c.525+2379A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,052 control chromosomes in the GnomAD database, including 28,804 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (28804 hom., cov: 32)
• Consequence: OXR1 NM_001198533.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OXR1	NM_001198533.2	c.525+2379A>G		intron_variant		ENST00000517566.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OXR1	ENST00000517566.7	c.525+2379A>G		intron_variant		1	NM_001198533.2	P3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92060 AN: 151936 Hom.: 28760 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.585

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.606 AC: 92166 AN: 152052 Hom.: 28804 Cov.: 32 AF XY: 0.600 AC XY: 44578 AN XY: 74326

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.589

Alfa AF: 0.563 Hom.: 12153

Bravo AF: 0.619

Asia WGS AF: 0.657 AC: 2275 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs776965; hg19: chr8-107698966;