Variant rs7815824 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.459C>T(p.Ser153=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0359 in 1,614,024 control chromosomes in the GnomAD database, including 1,818 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 0.068 ( 605 hom., cov: 32)

Exomes 𝑓: 0.033 ( 1213 hom. )

Consequence

OPRK1
NM_000912.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.822

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:

(HGNC:):

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=-0.59).

BP7

Synonymous conserved (PhyloP=0.822 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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.459C>T	p.Ser153=	synonymous_variant	3/4	ENST00000265572.8	NP_000903.2
OPRK1	NM_001318497.2 linkuse as main transcript	c.459C>T	p.Ser153=	synonymous_variant	3/4		NP_001305426.1
OPRK1	NM_001282904.2 linkuse as main transcript	c.192C>T	p.Ser64=	synonymous_variant	4/5		NP_001269833.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRK1	ENST00000265572.8 linkuse as main transcript	c.459C>T	p.Ser153=	synonymous_variant	3/4	1	NM_000912.5	ENSP00000265572	P1	P41145-1
	ENST00000524425.1 linkuse as main transcript	n.671-7618G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0680

AC:

10333

AN:

152024

Hom.:

605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0378

Gnomad ASJ

AF:

0.0533

Gnomad EAS

AF:

0.0150

Gnomad SAS

AF:

0.00809

Gnomad FIN

AF:

0.0484

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0307

Gnomad OTH

AF:

0.0593

GnomAD3 exomes

AF:

0.0368

AC:

9253

AN:

251400

Hom.:

345

AF XY:

0.0339

AC XY:

4609

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.167

Gnomad AMR exome

AF:

0.0201

Gnomad ASJ exome

AF:

0.0524

Gnomad EAS exome

AF:

0.0173

Gnomad SAS exome

AF:

0.0101

Gnomad FIN exome

AF:

0.0488

Gnomad NFE exome

AF:

0.0301

Gnomad OTH exome

AF:

0.0346

GnomAD4 exome

AF:

0.0326

AC:

47670

AN:

1461882

Hom.:

1213

Cov.:

AF XY:

0.0315

AC XY:

22887

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.0230

Gnomad4 ASJ exome

AF:

0.0569

Gnomad4 EAS exome

AF:

0.0156

Gnomad4 SAS exome

AF:

0.0102

Gnomad4 FIN exome

AF:

0.0485

Gnomad4 NFE exome

AF:

0.0295

Gnomad4 OTH exome

AF:

0.0374

GnomAD4 genome

AF:

0.0680

AC:

10352

AN:

152142

Hom.:

605

Cov.:

AF XY:

0.0664

AC XY:

4944

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.162

Gnomad4 AMR

AF:

0.0377

Gnomad4 ASJ

AF:

0.0533

Gnomad4 EAS

AF:

0.0151

Gnomad4 SAS

AF:

0.00810

Gnomad4 FIN

AF:

0.0484

Gnomad4 NFE

AF:

0.0307

Gnomad4 OTH

AF:

0.0597

Alfa

AF:

0.0521

Hom.:

185

Bravo

AF:

0.0724

Asia WGS

AF:

0.0170

AC:

AN:

3478

EpiCase

AF:

0.0321

EpiControl

AF:

0.0301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.9

DANN

Benign

0.86

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