Variant rs16918875 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000912.5(OPRK1):c.846C>T(p.Val282=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 1,614,034 control chromosomes in the GnomAD database, including 2,711 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 0.069 ( 546 hom., cov: 32)

Exomes 𝑓: 0.049 ( 2165 hom. )

Consequence

OPRK1
NM_000912.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0250

Variant links:

Genes affected

OPRK1 (HGNC:8154): (opioid receptor kappa 1) This gene encodes an opioid receptor, which is a member of the 7 transmembrane-spanning G protein-coupled receptor family. It functions as a receptor for endogenous ligands, as well as a receptor for various synthetic opioids. Ligand binding results in inhibition of adenylate cyclase activity and neurotransmitter release. This opioid receptor plays a role in the perception of pain and mediating the hypolocomotor, analgesic and aversive actions of synthetic opioids. Variations in this gene have also been associated with alcohol dependence and opiate addiction. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Dec 2017]

OPRK1 links:

LOC105375836 (HGNC:):

LOC105375836 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=0.025 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
OPRK1	NM_000912.5 linkuse as main transcript	c.846C>T	p.Val282=	synonymous_variant	4/4	ENST00000265572.8	NP_000903.2
LOC105375836	XR_928877.2 linkuse as main transcript	n.2306G>A		non_coding_transcript_exon_variant	3/3
OPRK1	NM_001318497.2 linkuse as main transcript	c.846C>T	p.Val282=	synonymous_variant	4/4		NP_001305426.1
OPRK1	NM_001282904.2 linkuse as main transcript	c.579C>T	p.Val193=	synonymous_variant	5/5		NP_001269833.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRK1	ENST00000265572.8 linkuse as main transcript	c.846C>T	p.Val282=	synonymous_variant	4/4	1	NM_000912.5	ENSP00000265572	P1	P41145-1
	ENST00000524425.1 linkuse as main transcript	n.671-12934G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0692

AC:

10523

AN:

152088

Hom.:

545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0379

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0334

Gnomad FIN

AF:

0.0189

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.0465

Gnomad OTH

AF:

0.0579

GnomAD3 exomes

AF:

0.0429

AC:

10772

AN:

251210

Hom.:

380

AF XY:

0.0419

AC XY:

5688

AN XY:

135772

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.0243

Gnomad ASJ exome

AF:

0.0179

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0369

Gnomad FIN exome

AF:

0.0208

Gnomad NFE exome

AF:

0.0477

Gnomad OTH exome

AF:

0.0434

GnomAD4 exome

AF:

0.0490

AC:

71681

AN:

1461828

Hom.:

2165

Cov.:

AF XY:

0.0485

AC XY:

35297

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.0251

Gnomad4 ASJ exome

AF:

0.0188

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0372

Gnomad4 FIN exome

AF:

0.0231

Gnomad4 NFE exome

AF:

0.0514

Gnomad4 OTH exome

AF:

0.0508

GnomAD4 genome

AF:

0.0692

AC:

10534

AN:

152206

Hom.:

546

Cov.:

AF XY:

0.0672

AC XY:

5004

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.0379

Gnomad4 ASJ

AF:

0.0202

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0328

Gnomad4 FIN

AF:

0.0189

Gnomad4 NFE

AF:

0.0465

Gnomad4 OTH

AF:

0.0568

Alfa

AF:

0.0514

Hom.:

325

Bravo

AF:

0.0738

Asia WGS

AF:

0.0280

AC:

AN:

3478

EpiCase

AF:

0.0466

EpiControl

AF:

0.0495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

2.5

DANN

Benign

0.79

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over