Variant X-43767621-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000898.5(MAOB):c.1411-3T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 1,202,693 control chromosomes in the GnomAD database, including 1,485 homozygotes. There are 12,248 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.059 ( 363 hom., 1928 hem., cov: 23)

Exomes 𝑓: 0.024 ( 1122 hom. 10320 hem. )

Consequence

MAOB
NM_000898.5 splice_region, intron

Scores

Splicing: ADA: 0.0002508

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452

Variant links:

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]

MAOB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5 linkuse as main transcript	c.1411-3T>C		splice_region_variant, intron_variant		ENST00000378069.5	NP_000889.3	P27338-1
MAOB	XM_017029524.3 linkuse as main transcript	c.1363-3T>C		splice_region_variant, intron_variant			XP_016885013.1	B7Z242

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5 linkuse as main transcript	c.1411-3T>C		splice_region_variant, intron_variant		1	NM_000898.5	ENSP00000367309.4		P27338-1

Frequencies

GnomAD3 genomes

AF:

0.0592

AC:

6608

AN:

111541

Hom.:

360

Cov.:

AF XY:

0.0568

AC XY:

1916

AN XY:

33735

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0801

Gnomad ASJ

AF:

0.0215

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00844

Gnomad NFE

AF:

0.00350

Gnomad OTH

AF:

0.0560

GnomAD3 exomes

AF:

0.0580

AC:

10242

AN:

176450

Hom.:

472

AF XY:

0.0575

AC XY:

3564

AN XY:

62004

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.0934

Gnomad ASJ exome

AF:

0.0163

Gnomad EAS exome

AF:

0.143

Gnomad SAS exome

AF:

0.187

Gnomad FIN exome

AF:

0.00305

Gnomad NFE exome

AF:

0.00326

Gnomad OTH exome

AF:

0.0378

GnomAD4 exome

AF:

0.0238

AC:

25934

AN:

1091100

Hom.:

1122

Cov.:

AF XY:

0.0289

AC XY:

10320

AN XY:

357250

show subpopulations

Gnomad4 AFR exome

AF:

0.151

Gnomad4 AMR exome

AF:

0.0933

Gnomad4 ASJ exome

AF:

0.0171

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.181

Gnomad4 FIN exome

AF:

0.00342

Gnomad4 NFE exome

AF:

0.00246

Gnomad4 OTH exome

AF:

0.0373

GnomAD4 genome

AF:

0.0594

AC:

6628

AN:

111593

Hom.:

363

Cov.:

AF XY:

0.0570

AC XY:

1928

AN XY:

33797

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.0797

Gnomad4 ASJ

AF:

0.0215

Gnomad4 EAS

AF:

0.148

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.00245

Gnomad4 NFE

AF:

0.00350

Gnomad4 OTH

AF:

0.0652

Alfa

AF:

0.0326

Hom.:

227

Bravo

AF:

0.0690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.2

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00025

dbscSNV1_RF

Benign

0.042

SpliceAI score (max)

0.12

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over