rs4654327

Variant names:

• chr1-28863626-G-A
• rs4654327
• NM_000911.4:c.*343G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-28863626-G-A
• chr1-28863626-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000911.4(OPRD1):​c.*343G>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 0.509 in 272,194 control chromosomes in the GnomAD database, including 37,291 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 0.48 (18981 hom., cov: 33)
  • Exomes 𝑓: 0.54 (18310 hom.)
• Consequence: OPRD1 NM_000911.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 34 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.*343G>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.*343G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_000911.4	ENSP00000234961.2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73495 AN: 151980 Hom.: 18974 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.541 AC: 64940 AN: 120094 Hom.: 18310 Cov.: 0 AF XY: 0.541 AC XY: 32673 AN XY: 60418

African (AFR) AF: 0.310 AC: 1200 AN: 3876

American (AMR) AF: 0.594 AC: 2080 AN: 3504

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 2029 AN: 4702

East Asian (EAS) AF: 0.818 AC: 8325 AN: 10178

South Asian (SAS) AF: 0.702 AC: 1003 AN: 1428

European-Finnish (FIN) AF: 0.592 AC: 5763 AN: 9740

Middle Eastern (MID) AF: 0.437 AC: 300 AN: 686

European-Non Finnish (NFE) AF: 0.514 AC: 39952 AN: 77772

Other (OTH) AF: 0.522 AC: 4288 AN: 8208

GnomAD4 genome AF: 0.483 AC: 73531 AN: 152100 Hom.: 18981 Cov.: 33 AF XY: 0.497 AC XY: 36953 AN XY: 74380

African (AFR) AF: 0.320 AC: 13259 AN: 41478

American (AMR) AF: 0.559 AC: 8550 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1527 AN: 3466

East Asian (EAS) AF: 0.780 AC: 4029 AN: 5164

South Asian (SAS) AF: 0.680 AC: 3284 AN: 4828

European-Finnish (FIN) AF: 0.616 AC: 6526 AN: 10590

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34885 AN: 67978

Other (OTH) AF: 0.463 AC: 976 AN: 2108

Alfa AF: 0.499 Hom.: 51513

Bravo AF: 0.470

Asia WGS AF: 0.684 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.71
PhyloP100		-2.5
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: rs4654327; hg19: chr1-29190138;