chr6-154011017-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000520282.5(OPRM1):c.9G>T(p.Gln3His) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as drug response (no stars).
Frequency
Consequence
ENST00000520282.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRM1 | NM_001145279.4 | c.-2G>T | splice_region_variant, 5_prime_UTR_variant | 1/6 | |||
OPRM1 | NM_001145280.4 | c.-12G>T | splice_region_variant, 5_prime_UTR_variant | 1/4 | |||
OPRM1 | NM_001145281.3 | c.47+458G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRM1 | ENST00000520282.5 | c.9G>T | p.Gln3His | missense_variant, splice_region_variant | 1/3 | 1 | |||
OPRM1 | ENST00000434900.6 | c.-2G>T | splice_region_variant, 5_prime_UTR_variant | 1/6 | 1 | ||||
OPRM1 | ENST00000520708.5 | c.-12G>T | splice_region_variant, 5_prime_UTR_variant | 1/4 | 1 | ||||
OPRM1 | ENST00000518759.5 | c.47+458G>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Tramadol response Other:1
drug response, no assertion criteria provided | research | Bruce Budowle Laboratory, University of North Texas Health Science Center | Apr 28, 2018 | - T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1 |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at