6-154107531-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1
The ENST00000419506.6(OPRM1):c.1231C>T(p.Gln411Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 718,426 control chromosomes in the GnomAD database, including 17,560 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3490 hom., cov: 32)
Exomes 𝑓: 0.22 ( 14070 hom. )
Consequence
OPRM1
ENST00000419506.6 stop_gained
ENST00000419506.6 stop_gained
Scores
7
Clinical Significance
Conservation
PhyloP100: -0.685
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 -8 ACMG points.
PM4
?
Stoplost variant in ENST00000419506.6 Downstream stopcodon found after 436 codons.
BP6
?
Variant 6-154107531-C-T is Benign according to our data. Variant chr6-154107531-C-T is described in ClinVar as [Benign]. Clinvar id is 403268.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRM1 | NM_000914.5 | c.1165-11152C>T | intron_variant | ENST00000330432.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRM1 | ENST00000330432.12 | c.1165-11152C>T | intron_variant | 1 | NM_000914.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31411AN: 152066Hom.: 3487 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.195 AC: 29485AN: 151582Hom.: 3161 AF XY: 0.196 AC XY: 15800AN XY: 80618
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GnomAD4 exome AF: 0.216 AC: 122057AN: 566240Hom.: 14070 Cov.: 0 AF XY: 0.215 AC XY: 65748AN XY: 305474
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GnomAD4 genome ? AF: 0.207 AC: 31444AN: 152186Hom.: 3490 Cov.: 32 AF XY: 0.201 AC XY: 14973AN XY: 74422
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 360/2178=16.5% - |
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:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
P;P;P;P;P;P;P;P;P;P;P;P
Vest4
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at