rs2298896

chr1-28839626-T-G

Variant summary

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

The NM_000911.4(OPRD1):c.228-19328T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,986 control chromosomes in the GnomAD database, including 9,164 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 0.34 (9164 hom., cov: 32)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786

Genes affected

OPRD1 (HGNC:8153): (opioid receptor delta 1) Enables G protein-coupled enkephalin receptor activity. Involved in several processes, including G protein-coupled opioid receptor signaling pathway; cellular response to hypoxia; and positive regulation of peptidyl-serine phosphorylation. Is intrinsic component of plasma membrane. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPRD1	NM_000911.4	c.228-19328T>G		intron_variant		ENST00000234961.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPRD1	ENST00000234961.7	c.228-19328T>G		intron_variant		1	NM_000911.4	P1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52131 AN: 151866 Hom.: 9160 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.343 AC: 52163 AN: 151986 Hom.: 9164 Cov.: 32 AF XY: 0.341 AC XY: 25346 AN XY: 74302

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.377

Alfa AF: 0.332 Hom.: 4001

Bravo AF: 0.353

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.70

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: rs2298896; hg19: chr1-29166138;