rs10521432

Positions:

• chrX-43774493-G-A

Variant summary

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

The NM_000898.5(MAOB):​c.1235+682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 110,553 control chromosomes in the GnomAD database, including 3,886 homozygotes. There are 9,276 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 0.30 (3886 hom., 9276 hem., cov: 22)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1235+682C>T		intron_variant		ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1187+682C>T		intron_variant			XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.1235+682C>T		intron_variant		1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.298 AC: 32899 AN: 110507 Hom.: 3884 Cov.: 22 AF XY: 0.282 AC XY: 9256 AN XY: 32807

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.0776

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.298 AC: 32919 AN: 110553 Hom.: 3886 Cov.: 22 AF XY: 0.282 AC XY: 9276 AN XY: 32863

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.317

Alfa AF: 0.288 Hom.: 17179

Bravo AF: 0.300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.25

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: rs10521432; hg19: chrX-43633740;