X-43768752-T-C

Variant names:

• chrX-43768752-T-C
• rs1799836
• NM_000898.5:c.1348-36A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 134 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000898.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	NM_000898.5	MANE Select	c.1348-36A>G		intron	N/A	NP_000889.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	ENST00000378069.5	TSL:1 MANE Select	c.1348-36A>G		intron	N/A	ENSP00000367309.4	P27338-1
	MAOB	ENST00000890313.1		c.1453-36A>G		intron	N/A	ENSP00000560372.1
	MAOB	ENST00000890309.1		c.1348-18A>G		intron	N/A	ENSP00000560368.1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 57512 AN: 109964 Hom.: 12038 Cov.: 22

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

GnomAD2 exomes AF: 0.426 AC: 75297 AN: 176852 AF XY: 0.417

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 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

African (AFR) AF: 0.783 AC: 19501 AN: 24895

American (AMR) AF: 0.351 AC: 12227 AN: 34848

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 7995 AN: 18722

East Asian (EAS) AF: 0.166 AC: 4898 AN: 29510

South Asian (SAS) AF: 0.346 AC: 17813 AN: 51465

European-Finnish (FIN) AF: 0.437 AC: 17594 AN: 40244

Middle Eastern (MID) AF: 0.485 AC: 1897 AN: 3915

European-Non Finnish (NFE) AF: 0.472 AC: 355938 AN: 754312

Other (OTH) AF: 0.462 AC: 19773 AN: 42839

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

African (AFR) AF: 0.767 AC: 23172 AN: 30201

American (AMR) AF: 0.407 AC: 4204 AN: 10324

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1102 AN: 2621

East Asian (EAS) AF: 0.171 AC: 593 AN: 3459

South Asian (SAS) AF: 0.328 AC: 845 AN: 2580

European-Finnish (FIN) AF: 0.422 AC: 2438 AN: 5782

Middle Eastern (MID) AF: 0.540 AC: 114 AN: 211

European-Non Finnish (NFE) AF: 0.457 AC: 24047 AN: 52658

Other (OTH) AF: 0.503 AC: 761 AN: 1512

Alfa AF: 0.477 Hom.: 48171

Bravo AF: 0.533

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.65
DANN	Benign	0.72
PhyloP100		-0.076
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: rs1799836; hg19: chrX-43627999;