chr8-106607325-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198533.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXR1	NM_001198533.2	MANE Select	c.221-71885C>G		intron	N/A	NP_001185462.1
	OXR1	NM_001198532.1		c.224-71885C>G		intron	N/A	NP_001185461.1
	OXR1	NM_018002.3		c.221-71885C>G		intron	N/A	NP_060472.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXR1	ENST00000517566.7	TSL:1 MANE Select	c.221-71885C>G		intron	N/A	ENSP00000429205.2
	OXR1	ENST00000442977.6	TSL:2	c.224-71885C>G		intron	N/A	ENSP00000405424.2
	OXR1	ENST00000531443.6	TSL:5	c.221-71885C>G		intron	N/A	ENSP00000431966.1

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

African (AFR) AF: 0.265 AC: 10980 AN: 41496

American (AMR) AF: 0.195 AC: 2983 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1946 AN: 5172

South Asian (SAS) AF: 0.144 AC: 695 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9873 AN: 68016

Other (OTH) AF: 0.195 AC: 411 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.29
DANN	Benign	0.71
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1564117; hg19: chr8-107619553;