rs165599
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000754(COMT):c.*522G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151920 control chromosomes in the gnomAD Genomes database, including 25878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).
Frequency
Genomes: 𝑓 0.56 ( 25878 hom., cov: 33)
Consequence
COMT
NM_000754 3_prime_UTR
NM_000754 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0760
Links
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
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COMT | NM_000754.4 | c.*522G>A | 3_prime_UTR_variant | 6/6 | ENST00000361682.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COMT | ENST00000361682.11 | c.*522G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_000754.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.560 AC: 85081AN: 151920Hom.: 25878 Cov.: 33
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GnomAD4 exome AF: 0.589 AC: 1456AN: 2474Hom.: 446 AF XY: 0.576 AC XY: 794AN XY: 1378
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ClinVar
Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
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
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at