X-43810702-A-G

Variant names:

• chrX-43810702-A-G
• rs12394221
• NM_000898.5:c.280-7298T>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.280-7298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 111,865 control chromosomes in the GnomAD database, including 423 homozygotes. There are 2,051 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 0.064 (423 hom., 2051 hem., cov: 23)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.280-7298T>C		intron_variant	Intron 3 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.232-7298T>C		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.280-7298T>C		intron_variant	Intron 3 of 14	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000487544.1	n.606-7298T>C		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 7109 AN: 111812 Hom.: 421 Cov.: 23

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0166

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.00164

Gnomad MID AF: 0.00840

Gnomad NFE AF: 0.00355

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0637 AC: 7127 AN: 111865 Hom.: 423 Cov.: 23 AF XY: 0.0602 AC XY: 2051 AN XY: 34055

African (AFR) AF: 0.184 AC: 5647 AN: 30643

American (AMR) AF: 0.0287 AC: 304 AN: 10597

Ashkenazi Jewish (ASJ) AF: 0.0166 AC: 44 AN: 2648

East Asian (EAS) AF: 0.101 AC: 357 AN: 3538

South Asian (SAS) AF: 0.174 AC: 463 AN: 2654

European-Finnish (FIN) AF: 0.00164 AC: 10 AN: 6083

Middle Eastern (MID) AF: 0.00922 AC: 2 AN: 217

European-Non Finnish (NFE) AF: 0.00355 AC: 189 AN: 53260

Other (OTH) AF: 0.0723 AC: 111 AN: 1536

Alfa AF: 0.0125 Hom.: 428

Bravo AF: 0.0722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.58
DANN	Benign	0.37
PhyloP100		-0.59
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: rs12394221; hg19: chrX-43669949;