rs2283729

chrX-43818795-G-AchrX-43818795-G-C

Variant summary

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

The NM_000898.5(MAOB):c.280-15391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 110,582 control chromosomes in the GnomAD database, including 3,636 homozygotes. There are 9,101 hemizygotes in GnomAD. 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 0.29 (3636 hom., 9101 hem., cov: 22)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

MAOB (HGNC:6834): (monoamine oxidase B) The protein encoded by this gene belongs to the flavin monoamine oxidase family. It is a enzyme located in the mitochondrial outer membrane. It catalyzes the oxidative deamination of biogenic and xenobiotic amines and plays an important role in the metabolism of neuroactive and vasoactive amines in the central nervous sysytem and peripheral tissues. This protein preferentially degrades benzylamine and phenylethylamine. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5	c.280-15391C>T		intron_variant		ENST00000378069.5
MAOB	XM_017029524.3	c.232-15391C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5	c.280-15391C>T		intron_variant		1	NM_000898.5	P1
MAOB	ENST00000487544.1	n.606-15391C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.290 AC: 32014 AN: 110524 Hom.: 3634 Cov.: 22 AF XY: 0.277 AC XY: 9073 AN XY: 32786

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0766

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.290 AC: 32040 AN: 110582 Hom.: 3636 Cov.: 22 AF XY: 0.277 AC XY: 9101 AN XY: 32854

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.310

Alfa AF: 0.281 Hom.: 15815

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.1
Dann	Benign	0.53

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: rs2283729; hg19: chrX-43678042;