rs16918900

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000265572.8(OPRK1):​c.610+77G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 1,257,100 control chromosomes in the GnomAD database, including 1,443 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 0.044 ( 166 hom., cov: 32)
Exomes 𝑓: 0.045 ( 1277 hom. )

Consequence

OPRK1
ENST00000265572.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0840
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OPRK1NM_000912.5 linkuse as main transcriptc.610+77G>A intron_variant ENST00000265572.8 NP_000903.2
OPRK1NM_001282904.2 linkuse as main transcriptc.343+77G>A intron_variant NP_001269833.1
OPRK1NM_001318497.2 linkuse as main transcriptc.610+77G>A intron_variant NP_001305426.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OPRK1ENST00000265572.8 linkuse as main transcriptc.610+77G>A intron_variant 1 NM_000912.5 ENSP00000265572 P1P41145-1
ENST00000524425.1 linkuse as main transcriptn.671-7846C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0441
AC:
6706
AN:
152138
Hom.:
166
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0640
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.0263
Gnomad ASJ
AF:
0.0205
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0330
Gnomad FIN
AF:
0.0186
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0457
Gnomad OTH
AF:
0.0387
GnomAD4 exome
AF:
0.0447
AC:
49379
AN:
1104844
Hom.:
1277
AF XY:
0.0446
AC XY:
24697
AN XY:
554352
show subpopulations
Gnomad4 AFR exome
AF:
0.0619
Gnomad4 AMR exome
AF:
0.0194
Gnomad4 ASJ exome
AF:
0.0181
Gnomad4 EAS exome
AF:
0.000186
Gnomad4 SAS exome
AF:
0.0374
Gnomad4 FIN exome
AF:
0.0228
Gnomad4 NFE exome
AF:
0.0500
Gnomad4 OTH exome
AF:
0.0438
GnomAD4 genome
AF:
0.0440
AC:
6703
AN:
152256
Hom.:
166
Cov.:
32
AF XY:
0.0419
AC XY:
3117
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0639
Gnomad4 AMR
AF:
0.0262
Gnomad4 ASJ
AF:
0.0205
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0326
Gnomad4 FIN
AF:
0.0186
Gnomad4 NFE
AF:
0.0457
Gnomad4 OTH
AF:
0.0378
Alfa
AF:
0.0447
Hom.:
147
Bravo
AF:
0.0451
Asia WGS
AF:
0.0210
AC:
72
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.7
DANN
Benign
0.61

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.

Other links and lift over

dbSNP: rs16918900; hg19: chr8-54147242; API