rs10753331

Positions:

• chr1-28838070-G-A
• chr1-28838070-G-T

Variant summary

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

The NM_000911.4(OPRD1):​c.228-20884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,214 control chromosomes in the GnomAD database, including 12,379 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 0.39 (12379 hom., cov: 29)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.228-20884G>A		intron_variant		ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.228-20884G>A		intron_variant		1	NM_000911.4	ENSP00000234961	P1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58721 AN: 151096 Hom.: 12365 Cov.: 29

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.389 AC: 58766 AN: 151214 Hom.: 12379 Cov.: 29 AF XY: 0.385 AC XY: 28396 AN XY: 73816

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.407

Alfa AF: 0.354 Hom.: 3969

Bravo AF: 0.405

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.72

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: rs10753331; hg19: chr1-29164582;