22-19947476-T-C

Variant names:

• chr22-19947476-T-C
• rs174680
• NM_000754.4:c.-92+5579T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000754.4(COMT):​c.-92+5579T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,826 control chromosomes in the GnomAD database, including 37,199 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 0.70 (37199 hom., cov: 31)
• Consequence: COMT NM_000754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 5 publications found

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]

COMT Gene-Disease associations (from GenCC):

• paroxysmal dyskinesia

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000754.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMT	NM_000754.4	MANE Select	c.-92+5579T>C		intron	N/A	NP_000745.1	P21964-1
	COMT	NM_001362828.2		c.-386+5579T>C		intron	N/A	NP_001349757.1	P21964-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMT	ENST00000361682.11	TSL:1 MANE Select	c.-92+5579T>C		intron	N/A	ENSP00000354511.6	P21964-1
	COMT	ENST00000678868.1		c.-106T>C		5_prime_UTR	Exon 2 of 7	ENSP00000503583.1	P21964-1
	COMT	ENST00000964897.1		c.-92+5579T>C		intron	N/A	ENSP00000634956.1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105920 AN: 151710 Hom.: 37183 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.698 AC: 105984 AN: 151826 Hom.: 37199 Cov.: 31 AF XY: 0.693 AC XY: 51398 AN XY: 74194

African (AFR) AF: 0.728 AC: 30181 AN: 41432

American (AMR) AF: 0.587 AC: 8961 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2477 AN: 3464

East Asian (EAS) AF: 0.563 AC: 2895 AN: 5140

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7488 AN: 10570

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48709 AN: 67830

Other (OTH) AF: 0.666 AC: 1407 AN: 2114

Alfa AF: 0.640 Hom.: 2073

Bravo AF: 0.688

Asia WGS AF: 0.610 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs174680; hg19: chr22-19934999;