rs10521432

Variant names:

• chrX-43774493-G-A
• rs10521432
• NM_000898.5:c.1235+682C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1235+682C>T		intron_variant	Intron 12 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1187+682C>T		intron_variant	Intron 12 of 14		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.1235+682C>T		intron_variant	Intron 12 of 14	1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.298 AC: 32899 AN: 110507 Hom.: 3884 Cov.: 22

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

African (AFR) AF: 0.400 AC: 12138 AN: 30325

American (AMR) AF: 0.188 AC: 1973 AN: 10481

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 826 AN: 2622

East Asian (EAS) AF: 0.110 AC: 386 AN: 3515

South Asian (SAS) AF: 0.273 AC: 714 AN: 2612

European-Finnish (FIN) AF: 0.232 AC: 1340 AN: 5788

Middle Eastern (MID) AF: 0.410 AC: 87 AN: 212

European-Non Finnish (NFE) AF: 0.283 AC: 14924 AN: 52806

Other (OTH) AF: 0.317 AC: 478 AN: 1509

Alfa AF: 0.296 Hom.: 24457

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
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10521432; hg19: chrX-43633740;