rs16837730

Positions:

• chr1-28853502-C-T

Variant summary

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

The ENST00000234961.7(OPRD1):​c.228-5452C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0559 in 152,282 control chromosomes in the GnomAD database, including 248 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 0.056 (248 hom., cov: 32)
• Consequence: OPRD1 ENST00000234961.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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 (SAS) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.228-5452C>T		intron_variant		ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.228-5452C>T		intron_variant		1	NM_000911.4	ENSP00000234961	P1

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8510 AN: 152164 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0559 AC: 8515 AN: 152282 Hom.: 248 Cov.: 32 AF XY: 0.0544 AC XY: 4053 AN XY: 74454

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.0403

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.0823

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.0189

Gnomad4 NFE AF: 0.0502

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0533 Hom.: 99

Bravo AF: 0.0578

Asia WGS AF: 0.0910 AC: 316 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	0.68
DANN	Benign	0.59

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: rs16837730; hg19: chr1-29180014;