rs204081

Positions:

• chr1-28860207-G-A
• chr1-28860207-G-C
• chr1-28860207-G-T

Variant summary

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

The NM_000911.4(OPRD1):​c.577+904G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,914 control chromosomes in the GnomAD database, including 39,496 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 0.72 (39496 hom., cov: 30)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.577+904G>A		intron_variant		ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.577+904G>A		intron_variant		1	NM_000911.4	ENSP00000234961	P1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108792 AN: 151796 Hom.: 39463 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.717 AC: 108883 AN: 151914 Hom.: 39496 Cov.: 30 AF XY: 0.727 AC XY: 54008 AN XY: 74244

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.701

Alfa AF: 0.592 Hom.: 1665

Bravo AF: 0.721

Asia WGS AF: 0.857 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.55

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: rs204081; hg19: chr1-29186719;