rs1485471

Positions:

• chr1-28868389-C-T

Variant summary

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

The NM_000911.4(OPRD1):​c.*5106C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,226 control chromosomes in the GnomAD database, including 6,716 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 0.26 (6716 hom., cov: 33)
  • Exomes 𝑓: 0.29 (0 hom.)
• Consequence: OPRD1 NM_000911.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.*5106C>T		3_prime_UTR_variant	3/3	ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.*5106C>T		3_prime_UTR_variant	3/3	1	NM_000911.4	ENSP00000234961	P1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40254 AN: 152094 Hom.: 6712 Cov.: 33

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.258

GnomAD4 exome AF: 0.286 AC: 4 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.265 AC: 40266 AN: 152212 Hom.: 6716 Cov.: 33 AF XY: 0.271 AC XY: 20185 AN XY: 74416

Gnomad4 AFR AF: 0.0719

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.0701

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.261

Alfa AF: 0.329 Hom.: 15250

Bravo AF: 0.242

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.57

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: rs1485471; hg19: chr1-29194901;