rs2283729

Variant names:

• chrX-43818795-G-A
• rs2283729
• NM_000898.5:c.280-15391C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-43818795-G-A
• chrX-43818795-G-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.280-15391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 110,582 control chromosomes in the GnomAD database, including 3,636 homozygotes. There are 9,101 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 0.29 (3636 hom., 9101 hem., cov: 22)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 10 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.280-15391C>T		intron_variant	Intron 3 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.232-15391C>T		intron_variant	Intron 3 of 14		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.280-15391C>T		intron_variant	Intron 3 of 14	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000487544.1	n.606-15391C>T		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.290 AC: 32014 AN: 110524 Hom.: 3634 Cov.: 22

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0766

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.290 AC: 32040 AN: 110582 Hom.: 3636 Cov.: 22 AF XY: 0.277 AC XY: 9101 AN XY: 32854

African (AFR) AF: 0.376 AC: 11411 AN: 30379

American (AMR) AF: 0.187 AC: 1953 AN: 10469

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 811 AN: 2618

East Asian (EAS) AF: 0.126 AC: 447 AN: 3536

South Asian (SAS) AF: 0.276 AC: 726 AN: 2628

European-Finnish (FIN) AF: 0.225 AC: 1330 AN: 5913

Middle Eastern (MID) AF: 0.418 AC: 89 AN: 213

European-Non Finnish (NFE) AF: 0.280 AC: 14757 AN: 52680

Other (OTH) AF: 0.310 AC: 467 AN: 1506

Alfa AF: 0.283 Hom.: 22373

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		1.2
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: rs2283729; hg19: chrX-43678042;