rs7815824
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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
NM_000912.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.822
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 -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
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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 | UniProt |
---|---|---|---|---|---|---|---|
OPRK1 | NM_000912.5 | c.459C>T | p.Ser153= | synonymous_variant | 3/4 | ENST00000265572.8 | |
OPRK1 | NM_001318497.2 | c.459C>T | p.Ser153= | synonymous_variant | 3/4 | ||
OPRK1 | NM_001282904.2 | c.192C>T | p.Ser64= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRK1 | ENST00000265572.8 | c.459C>T | p.Ser153= | synonymous_variant | 3/4 | 1 | NM_000912.5 | P1 | |
ENST00000524425.1 | n.671-7618G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0680 AC: 10333AN: 152024Hom.: 605 Cov.: 32
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GnomAD3 exomes AF: 0.0368 AC: 9253AN: 251400Hom.: 345 AF XY: 0.0339 AC XY: 4609AN XY: 135892
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GnomAD4 exome AF: 0.0326 AC: 47670AN: 1461882Hom.: 1213 Cov.: 31 AF XY: 0.0315 AC XY: 22887AN XY: 727242
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GnomAD4 genome ? AF: 0.0680 AC: 10352AN: 152142Hom.: 605 Cov.: 32 AF XY: 0.0664 AC XY: 4944AN XY: 74404
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at