22-19946502-A-G

Position:

• chr22-19946502-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.-92+4605A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,956 control chromosomes in the GnomAD database, including 34,855 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 0.67 (34855 hom., cov: 31)
• Consequence: COMT NM_000754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COMT	NM_000754.4	c.-92+4605A>G		intron_variant		ENST00000361682.11	NP_000745.1
COMT	NM_001362828.2	c.-386+4605A>G		intron_variant			NP_001349757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMT	ENST00000361682.11	c.-92+4605A>G		intron_variant		1	NM_000754.4	ENSP00000354511	P2

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102492 AN: 151838 Hom.: 34844 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.675 AC: 102550 AN: 151956 Hom.: 34855 Cov.: 31 AF XY: 0.670 AC XY: 49771 AN XY: 74248

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.653

Alfa AF: 0.707 Hom.: 36926

Bravo AF: 0.660

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.9
DANN	Benign	0.84

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: rs174674; hg19: chr22-19934025;