rs204076

chr1-28863878-T-Achr1-28863878-T-Cchr1-28863878-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.*595T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,256 control chromosomes in the GnomAD database, including 41,118 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 0.73 (41089 hom., cov: 31)
  • Exomes 𝑓: 0.61 (29 hom.)
• Consequence: OPRD1 NM_000911.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPRD1	NM_000911.4	c.*595T>A		3_prime_UTR_variant	3/3	ENST00000234961.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPRD1	ENST00000234961.7	c.*595T>A		3_prime_UTR_variant	3/3	1	NM_000911.4	P1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110754 AN: 151978 Hom.: 41042 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.706

GnomAD4 exome AF: 0.614 AC: 97 AN: 158 Hom.: 29 Cov.: 0 AF XY: 0.618 AC XY: 68 AN XY: 110

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.667

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.729 AC: 110858 AN: 152098 Hom.: 41089 Cov.: 31 AF XY: 0.740 AC XY: 54998 AN XY: 74342

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.708

Alfa AF: 0.694 Hom.: 4365

Bravo AF: 0.735

Asia WGS AF: 0.862 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.31
Dann	Benign	0.54

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: rs204076; hg19: chr1-29190390;