1-28860207-G-A

Variant names:

• chr1-28860207-G-A
• rs204081
• NM_000911.4:c.577+904G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.577+904G>A		intron_variant	Intron 2 of 2	ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.577+904G>A		intron_variant	Intron 2 of 2	1	NM_000911.4	ENSP00000234961.2

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

African (AFR) AF: 0.789 AC: 32659 AN: 41418

American (AMR) AF: 0.781 AC: 11916 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3468

East Asian (EAS) AF: 0.909 AC: 4703 AN: 5174

South Asian (SAS) AF: 0.820 AC: 3938 AN: 4804

European-Finnish (FIN) AF: 0.731 AC: 7731 AN: 10570

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43561 AN: 67926

Other (OTH) AF: 0.701 AC: 1473 AN: 2100

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs204081; hg19: chr1-29186719;