rs7826614
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000912.5(OPRK1):c.257+5915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,002 control chromosomes in the GnomAD database, including 3,271 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 0.20 ( 3271 hom., cov: 32)
Consequence
OPRK1
NM_000912.5 intron
NM_000912.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.136
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=-1.04).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRK1 | NM_000912.5 | c.257+5915C>T | intron_variant | ENST00000265572.8 | |||
OPRK1 | NM_001282904.2 | c.-184-1954C>T | intron_variant | ||||
OPRK1 | NM_001318497.2 | c.257+5915C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRK1 | ENST00000265572.8 | c.257+5915C>T | intron_variant | 1 | NM_000912.5 | P1 | |||
OPRK1 | ENST00000520287.5 | c.257+5915C>T | intron_variant | 1 | P1 | ||||
OPRK1 | ENST00000522508.1 | c.258-1954C>T | intron_variant, NMD_transcript_variant | 1 | |||||
OPRK1 | ENST00000673285.2 | c.257+5915C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30231AN: 151884Hom.: 3269 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.199 AC: 30249AN: 152002Hom.: 3271 Cov.: 32 AF XY: 0.200 AC XY: 14887AN XY: 74300
GnomAD4 genome
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908
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at