rs3027452

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-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 AF XY: 0.130 AC XY: 4306 AN XY: 33183

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

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.129

Alfa AF: 0.161 Hom.: 6257

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

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: rs3027452; hg19: chrX-43657789;