Menu
GeneBe

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

Scores

2

Clinical Significance

drug response no assertion criteria provided O:1

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
COMTNM_000754.4 linkuse as main transcriptc.*522G>A 3_prime_UTR_variant 6/6 ENST00000361682.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COMTENST00000361682.11 linkuse as main transcriptc.*522G>A 3_prime_UTR_variant 6/61 NM_000754.4 P2P21964-1

Frequencies

GnomAD3 genomes
AF:
0.560
AC:
85081
AN:
151920
Hom.:
25878
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.316
Gnomad AMI
AF:
0.796
Gnomad AMR
AF:
0.541
Gnomad ASJ
AF:
0.609
Gnomad EAS
AF:
0.499
Gnomad SAS
AF:
0.568
Gnomad FIN
AF:
0.668
Gnomad MID
AF:
0.655
Gnomad NFE
AF:
0.694
Gnomad OTH
AF:
0.580
GnomAD4 exome
AF:
0.589
AC:
1456
AN:
2474
Hom.:
446
AF XY:
0.576
AC XY:
794
AN XY:
1378
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.452
Gnomad4 ASJ exome
AF:
0.556
Gnomad4 EAS exome
AF:
0.583
Gnomad4 SAS exome
AF:
0.474
Gnomad4 FIN exome
AF:
0.586
Gnomad4 NFE exome
AF:
0.640
Gnomad4 OTH exome
AF:
0.589
Alfa
AF:
0.665
Hom.:
51250
Bravo
AF:
0.538
Asia WGS
AF:
0.531
AC:
1846
AN:
3478

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 providedresearchBruce Budowle Laboratory, University of North Texas Health Science CenterApr 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
1.8
Dann
Benign
0.47

Splicing

Find out SpliceAI and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs165599; hg19: chr22-19956781;