NM_000898.5:c.1236-1536A>C

Variant names:

• chrX-43770954-T-G
• rs2239449
• NM_000898.5:c.1236-1536A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1236-1536A>C		intron_variant	Intron 12 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1188-1536A>C		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.1236-1536A>C		intron_variant	Intron 12 of 14	1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 5222 AN: 111564 Hom.: 210 Cov.: 23

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

African (AFR) AF: 0.103 AC: 3141 AN: 30606

American (AMR) AF: 0.0734 AC: 771 AN: 10507

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 54 AN: 2644

East Asian (EAS) AF: 0.149 AC: 521 AN: 3506

South Asian (SAS) AF: 0.180 AC: 470 AN: 2615

European-Finnish (FIN) AF: 0.00229 AC: 14 AN: 6107

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.00355 AC: 189 AN: 53211

Other (OTH) AF: 0.0520 AC: 79 AN: 1518

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
PhyloP100		-0.44
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: rs2239449; hg19: chrX-43630201;