rs740603

chr22-19957654-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000754.4(COMT):c.-91-3545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,124 control chromosomes in the GnomAD database, including 18,028 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18028 hom., cov: 33)
• Consequence: COMT NM_000754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

Genes affected

COMT (HGNC:2228): (catechol-O-methyltransferase) Catechol-O-methyltransferase catalyzes the transfer of a methyl group from S-adenosylmethionine to catecholamines, including the neurotransmitters dopamine, epinephrine, and norepinephrine. This O-methylation results in one of the major degradative pathways of the catecholamine transmitters. In addition to its role in the metabolism of endogenous substances, COMT is important in the metabolism of catechol drugs used in the treatment of hypertension, asthma, and Parkinson disease. COMT is found in two forms in tissues, a soluble form (S-COMT) and a membrane-bound form (MB-COMT). The differences between S-COMT and MB-COMT reside within the N-termini. Several transcript variants are formed through the use of alternative translation initiation sites and promoters. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COMT	NM_000754.4	c.-91-3545A>G		intron_variant		ENST00000361682.11
COMT	NM_001135161.2	c.-91-3545A>G		intron_variant
COMT	NM_001135162.2	c.-91-3545A>G		intron_variant
COMT	NM_001362828.2	c.-385-3545A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COMT	ENST00000361682.11	c.-91-3545A>G		intron_variant		1	NM_000754.4	P2

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73303 AN: 152006 Hom.: 18014 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.544

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.482 AC: 73355 AN: 152124 Hom.: 18028 Cov.: 33 AF XY: 0.477 AC XY: 35480 AN XY: 74366

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.543

Alfa AF: 0.529 Hom.: 34831

Bravo AF: 0.486

Asia WGS AF: 0.459 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.35
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs740603; hg19: chr22-19945177;