rs680090

Variant names:

• chr1-28848949-G-A
• rs680090
• NM_000911.4:c.228-10005G>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.228-10005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,000 control chromosomes in the GnomAD database, including 14,746 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 0.40 (14746 hom., cov: 31)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.228-10005G>A		intron_variant	Intron 1 of 2	ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.228-10005G>A		intron_variant	Intron 1 of 2	1	NM_000911.4	ENSP00000234961.2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61455 AN: 151882 Hom.: 14739 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.404 AC: 61480 AN: 152000 Hom.: 14746 Cov.: 31 AF XY: 0.413 AC XY: 30670 AN XY: 74292

African (AFR) AF: 0.157 AC: 6529 AN: 41482

American (AMR) AF: 0.449 AC: 6848 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4489 AN: 5164

South Asian (SAS) AF: 0.621 AC: 2985 AN: 4806

European-Finnish (FIN) AF: 0.534 AC: 5645 AN: 10564

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32039 AN: 67944

Other (OTH) AF: 0.383 AC: 809 AN: 2110

Alfa AF: 0.388 Hom.: 1976

Bravo AF: 0.382

Asia WGS AF: 0.675 AC: 2345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.26
PhyloP100		0.11
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: rs680090; hg19: chr1-29175461;