rs3027459

Variant names:

• chrX-43802030-C-T
• rs3027459
• NM_000898.5:c.476+142G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000898.5(MAOB):​c.476+142G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00537 in 513,104 control chromosomes in the GnomAD database, including 47 homozygotes. There are 713 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 0.016 (34 hom., 490 hem., cov: 24)
  • Exomes 𝑓: 0.0023 (13 hom. 223 hem.)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.476+142G>A		intron_variant	Intron 5 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.428+142G>A		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.476+142G>A		intron_variant	Intron 5 of 14	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000487544.1	n.802+142G>A		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0162 AC: 1829 AN: 112826 Hom.: 34 Cov.: 24 AF XY: 0.0140 AC XY: 490 AN XY: 34978

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00617

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00418

Gnomad NFE AF: 0.000150

Gnomad OTH AF: 0.0145

GnomAD4 exome AF: 0.00231 AC: 923 AN: 400227 Hom.: 13 AF XY: 0.00164 AC XY: 223 AN XY: 135967

Gnomad4 AFR exome AF: 0.0569

Gnomad4 AMR exome AF: 0.00311

Gnomad4 ASJ exome AF: 0.0000761

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000894

Gnomad4 FIN exome AF: 0.0000377

Gnomad4 NFE exome AF: 0.000133

Gnomad4 OTH exome AF: 0.00412

GnomAD4 genome AF: 0.0162 AC: 1833 AN: 112877 Hom.: 34 Cov.: 24 AF XY: 0.0140 AC XY: 490 AN XY: 35039

Gnomad4 AFR AF: 0.0558

Gnomad4 AMR AF: 0.00616

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000150

Gnomad4 OTH AF: 0.0143

Alfa AF: 0.00382 Hom.: 84

Bravo AF: 0.0189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.86
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: rs3027459; hg19: chrX-43661277;