rs2239449

Positions:

• chrX-43770954-T-G

Variant summary

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

The NM_000898.5(MAOB):​c.1236-1536A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 111,618 control chromosomes in the GnomAD database, including 213 homozygotes. There are 1,570 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 0.047 (213 hom., 1570 hem., cov: 23)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

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 (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1236-1536A>C		intron_variant		ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1188-1536A>C		intron_variant			XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.1236-1536A>C		intron_variant		1	NM_000898.5	ENSP00000367309	P1

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 5222 AN: 111564 Hom.: 210 Cov.: 23 AF XY: 0.0462 AC XY: 1560 AN XY: 33764

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.00229

Gnomad MID AF: 0.00420

Gnomad NFE AF: 0.00355

Gnomad OTH AF: 0.0427

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

GnomAD4 genome AF: 0.0469 AC: 5239 AN: 111618 Hom.: 213 Cov.: 23 AF XY: 0.0464 AC XY: 1570 AN XY: 33828

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0734

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.00229

Gnomad4 NFE AF: 0.00355

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0309 Hom.: 142

Bravo AF: 0.0549

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.39

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: rs2239449; hg19: chrX-43630201;