rs5746849

Positions:

• chr22-19955474-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.-91-5725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,182 control chromosomes in the GnomAD database, including 19,551 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 0.50 (19551 hom., cov: 34)
• Consequence: COMT NM_000754.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COMT	NM_000754.4	c.-91-5725A>G		intron_variant		ENST00000361682.11	NP_000745.1
COMT	NM_001135161.2	c.-92+4422A>G		intron_variant			NP_001128633.1
COMT	NM_001135162.2	c.-92+3820A>G		intron_variant			NP_001128634.1
COMT	NM_001362828.2	c.-385-5725A>G		intron_variant			NP_001349757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMT	ENST00000361682.11	c.-91-5725A>G		intron_variant		1	NM_000754.4	ENSP00000354511	P2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76442 AN: 152064 Hom.: 19531 Cov.: 34

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.503 AC: 76505 AN: 152182 Hom.: 19551 Cov.: 34 AF XY: 0.496 AC XY: 36930 AN XY: 74386

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.549

Alfa AF: 0.506 Hom.: 3484

Bravo AF: 0.509

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.26

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: rs5746849; hg19: chr22-19942997;