rs16918900
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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
ENST00000265572.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0840
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 |
---|---|---|---|---|---|---|---|---|
OPRK1 | NM_000912.5 | c.610+77G>A | intron_variant | ENST00000265572.8 | NP_000903.2 | |||
OPRK1 | NM_001282904.2 | c.343+77G>A | intron_variant | NP_001269833.1 | ||||
OPRK1 | NM_001318497.2 | c.610+77G>A | intron_variant | NP_001305426.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OPRK1 | ENST00000265572.8 | c.610+77G>A | intron_variant | 1 | NM_000912.5 | ENSP00000265572 | P1 | |||
ENST00000524425.1 | n.671-7846C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0441 AC: 6706AN: 152138Hom.: 166 Cov.: 32
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GnomAD4 exome AF: 0.0447 AC: 49379AN: 1104844Hom.: 1277 AF XY: 0.0446 AC XY: 24697AN XY: 554352
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GnomAD4 genome AF: 0.0440 AC: 6703AN: 152256Hom.: 166 Cov.: 32 AF XY: 0.0419 AC XY: 3117AN XY: 74452
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at