NM_000911.4:c.*5023A>G

Variant names:

• chr1-28868306-A-G
• rs204069
• NM_000911.4:c.*5023A>G

Variant summary

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

The NM_000911.4(OPRD1):​c.*5023A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,058 control chromosomes in the GnomAD database, including 41,220 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 (41217 hom., cov: 32)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: OPRD1 NM_000911.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.*5023A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.*5023A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_000911.4	ENSP00000234961.2

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110936 AN: 151928 Hom.: 41174 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.703

GnomAD4 exome AF: 0.750 AC: 9 AN: 12 Hom.: 3 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 FIN exome AF: 1.00

Gnomad4 OTH exome AF: 0.625

GnomAD4 genome AF: 0.730 AC: 111035 AN: 152046 Hom.: 41217 Cov.: 32 AF XY: 0.741 AC XY: 55103 AN XY: 74332

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.704

Alfa AF: 0.664 Hom.: 58642

Bravo AF: 0.736

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.36

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: rs204069; hg19: chr1-29194818;