X-43768752-T-C

Position:

• chrX-43768752-T-C

Variant summary

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

The NM_000898.5(MAOB):​c.1348-36A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,110,769 control chromosomes in the GnomAD database, including 86,295 homozygotes. There are 154,346 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 0.52 (12043 hom., 16191 hem., cov: 22)
  • Exomes 𝑓: 0.46 (74252 hom. 138155 hem.)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1348-36A>G		intron_variant		ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1300-36A>G		intron_variant			XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.1348-36A>G		intron_variant		1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.523 AC: 57512 AN: 109964 Hom.: 12038 Cov.: 22 AF XY: 0.501 AC XY: 16146 AN XY: 32250

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.510

GnomAD3 exomes AF: 0.426 AC: 75297 AN: 176852 Hom.: 11736 AF XY: 0.417 AC XY: 25913 AN XY: 62116

Gnomad AFR exome AF: 0.777

Gnomad AMR exome AF: 0.340

Gnomad ASJ exome AF: 0.427

Gnomad EAS exome AF: 0.185

Gnomad SAS exome AF: 0.339

Gnomad FIN exome AF: 0.438

Gnomad NFE exome AF: 0.455

Gnomad OTH exome AF: 0.442

GnomAD4 exome AF: 0.457 AC: 457636 AN: 1000750 Hom.: 74252 Cov.: 19 AF XY: 0.472 AC XY: 138155 AN XY: 292908

Gnomad4 AFR exome AF: 0.783

Gnomad4 AMR exome AF: 0.351

Gnomad4 ASJ exome AF: 0.427

Gnomad4 EAS exome AF: 0.166

Gnomad4 SAS exome AF: 0.346

Gnomad4 FIN exome AF: 0.437

Gnomad4 NFE exome AF: 0.472

Gnomad4 OTH exome AF: 0.462

GnomAD4 genome AF: 0.523 AC: 57555 AN: 110019 Hom.: 12043 Cov.: 22 AF XY: 0.501 AC XY: 16191 AN XY: 32315

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.503

Alfa AF: 0.463 Hom.: 33567

Bravo AF: 0.533

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.65
DANN	Benign	0.72

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: rs1799836; hg19: chrX-43627999;