rs204076

Variant names:

• chr1-28863878-T-A
• rs204076
• NM_000911.4:c.*595T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-28863878-T-A
• chr1-28863878-T-C
• chr1-28863878-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 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=-0.97).
• 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 rank	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.*595T>A		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.*595T>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_000911.4	ENSP00000234961.2

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.667 AC: 4 AN: 6

European-Finnish (FIN) AF: 0.400 AC: 4 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.625 AC: 80 AN: 128

Other (OTH) AF: 0.500 AC: 3 AN: 6

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

African (AFR) AF: 0.836 AC: 34685 AN: 41510

American (AMR) AF: 0.792 AC: 12104 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4703 AN: 5172

South Asian (SAS) AF: 0.817 AC: 3946 AN: 4828

European-Finnish (FIN) AF: 0.730 AC: 7714 AN: 10568

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43366 AN: 67950

Other (OTH) AF: 0.708 AC: 1495 AN: 2112

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
PhyloP100		-2.6

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: rs204076; hg19: chr1-29190390;