8-106607325-C-G

Variant names:

• chr8-106607325-C-G
• rs1564117
• NM_001198533.2:c.221-71885C>G

Variant summary

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

The NM_001198533.2(OXR1):​c.221-71885C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,168 control chromosomes in the GnomAD database, including 3,146 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 0.19 (3146 hom., cov: 32)
• Consequence: OXR1 NM_001198533.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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]

OXR1-AS1 (HGNC:55533): (OXR1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OXR1	NM_001198533.2	c.221-71885C>G		intron_variant	Intron 3 of 16	ENST00000517566.7	NP_001185462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OXR1	ENST00000517566.7	c.221-71885C>G		intron_variant	Intron 3 of 16	1	NM_001198533.2	ENSP00000429205.2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29520 AN: 152050 Hom.: 3136 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.194 AC: 29552 AN: 152168 Hom.: 3146 Cov.: 32 AF XY: 0.194 AC XY: 14395 AN XY: 74386

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.195

Alfa AF: 0.168 Hom.: 270

Bravo AF: 0.205

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.29
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564117; hg19: chr8-107619553;