rs17181352
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000914.5(OPRM1):c.*725A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 985,388 control chromosomes in the GnomAD database, including 3 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 0.0010 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
OPRM1
NM_000914.5 3_prime_UTR
NM_000914.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.257
Genes affected
OPRM1 (HGNC:8156): (opioid receptor mu 1) This gene encodes one of at least three opioid receptors in humans; the mu opioid receptor (MOR). The MOR is the principal target of endogenous opioid peptides and opioid analgesic agents such as beta-endorphin and enkephalins. The MOR also has an important role in dependence to other drugs of abuse, such as nicotine, cocaine, and alcohol via its modulation of the dopamine system. The NM_001008503.2:c.118A>G allele has been associated with opioid and alcohol addiction and variations in pain sensitivity but evidence for it having a causal role is conflicting. Multiple transcript variants encoding different isoforms have been found for this gene. Though the canonical MOR belongs to the superfamily of 7-transmembrane-spanning G-protein-coupled receptors some isoforms of this gene have only 6 transmembrane domains. [provided by RefSeq, Oct 2013]
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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).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00103 (157/152294) while in subpopulation EAS AF= 0.0257 (133/5172). AF 95% confidence interval is 0.0222. There are 2 homozygotes in gnomad4. There are 83 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRM1 | NM_000914.5 | c.*725A>G | 3_prime_UTR_variant | 4/4 | ENST00000330432.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRM1 | ENST00000330432.12 | c.*725A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_000914.5 | P1 | ||
OPRM1 | ENST00000337049.8 | c.1164+27974A>G | intron_variant | 1 | |||||
OPRM1 | ENST00000524150.2 | c.*250+27974A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00103 AC: 157AN: 152176Hom.: 2 Cov.: 32
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GnomAD4 exome AF: 0.000164 AC: 137AN: 833094Hom.: 1 Cov.: 30 AF XY: 0.000122 AC XY: 47AN XY: 384702
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GnomAD4 genome ? AF: 0.00103 AC: 157AN: 152294Hom.: 2 Cov.: 32 AF XY: 0.00111 AC XY: 83AN XY: 74474
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at