rs1799971
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM1BP4_StrongBA1
The NM_000914(OPRM1):c.118A>G(p.Asn40Asp) variant causes a missense change. The variant allele was found at a frequency of 0.13 in 152054 control chromosomes in the gnomAD Genomes database, including 1912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance,drug response (no stars).
Frequency
Genomes: 𝑓 0.13 ( 1912 hom., cov: 32)
Exomes 𝑓: 0.19 ( 5913 hom. )
Consequence
OPRM1
NM_000914 missense
NM_000914 missense
Scores
4
12
Clinical Significance
Conservation
PhyloP100: 4.31
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM1
?
In a glycosylation_site N-linked (GlcNAc...) asparagine (size 0) in uniprot entity OPRM_HUMAN
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002016455).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRM1 | NM_000914.5 | c.118A>G | p.Asn40Asp | missense_variant | 1/4 | ENST00000330432.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRM1 | ENST00000330432.12 | c.118A>G | p.Asn40Asp | missense_variant | 1/4 | 1 | NM_000914.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19734AN: 152054Hom.: 1912 Cov.: 32
GnomAD3 genomes
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19734
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32
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GnomAD3 exomes AF: 0.188 AC: 46959AN: 249224Hom.: 5913 AF XY: 0.196 AC XY: 26451AN XY: 135238
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GnomAD4 exome AF: 0.153 AC: 223836AN: 1461520Hom.: 21864 AF XY: 0.159 AC XY: 115536AN XY: 726998
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TwinsUK
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479
ALSPAC
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489
ESP6500AA
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122
ESP6500EA
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1070
ExAC
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22379
Asia WGS
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1311
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3478
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ClinVar
Significance: Uncertain significance; drug response
Submissions summary: Uncertain:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Opioid dependence, susceptibility to, 1 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Jun 30, 2009 | - - |
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
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T;T;T;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P;P;P;P;P;P;P
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;.;D;D;D;D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;T;D;D;D;T;D;D;D
Polyphen
0.081, 0.23, 0.0070, 0.73, 0.49, 0.95, 0.0010, 0.22, 0.0030
.;B;.;B;B;P;P;P;B;P;B;B
Vest4
0.18, 0.097, 0.17, 0.18, 0.19, 0.19, 0.20, 0.22, 0.19, 0.19
MPC
0.11
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out SpliceAI and Pangolin per-transcript scores at