rs3027452

Variant names:

• chrX-43798542-G-A
• rs3027452
• NM_000898.5:c.477-1276C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000898.5(MAOB):​c.477-1276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 111,013 control chromosomes in the GnomAD database, including 833 homozygotes. There are 4,310 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 0.13 (833 hom., 4310 hem., cov: 22)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.477-1276C>T		intron_variant	Intron 5 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.429-1276C>T		intron_variant	Intron 5 of 14		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.477-1276C>T		intron_variant	Intron 5 of 14	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000487544.1	n.803-1276C>T		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 14538 AN: 110959 Hom.: 832 Cov.: 22

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0840

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.131 AC: 14538 AN: 111013 Hom.: 833 Cov.: 22 AF XY: 0.130 AC XY: 4310 AN XY: 33247

African (AFR) AF: 0.0278 AC: 854 AN: 30729

American (AMR) AF: 0.181 AC: 1888 AN: 10415

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 303 AN: 2644

East Asian (EAS) AF: 0.148 AC: 514 AN: 3484

South Asian (SAS) AF: 0.232 AC: 607 AN: 2615

European-Finnish (FIN) AF: 0.187 AC: 1103 AN: 5911

Middle Eastern (MID) AF: 0.0829 AC: 18 AN: 217

European-Non Finnish (NFE) AF: 0.167 AC: 8826 AN: 52800

Other (OTH) AF: 0.129 AC: 197 AN: 1526

Alfa AF: 0.156 Hom.: 8249

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.065
DANN	Benign	0.42
PhyloP100		-0.94
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: rs3027452; hg19: chrX-43657789;