Variant X-43802246-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_000898.5(MAOB):c.402A>G(p.Pro134=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,194,395 control chromosomes in the GnomAD database, including 4 homozygotes. There are 1,130 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., 68 hem., cov: 24)

Exomes 𝑓: 0.0031 ( 4 hom. 1062 hem. )

Consequence

MAOB
NM_000898.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.51

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant X-43802246-T-C is Benign according to our data. Variant chrX-43802246-T-C is described in ClinVar as [Benign]. Clinvar id is 717563.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-43802246-T-C is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-3.51 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 68 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5 linkuse as main transcript	c.402A>G	p.Pro134=	synonymous_variant	5/15	ENST00000378069.5
MAOB	XM_017029524.3 linkuse as main transcript	c.354A>G	p.Pro118=	synonymous_variant	5/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5 linkuse as main transcript	c.402A>G	p.Pro134=	synonymous_variant	5/15	1	NM_000898.5	P1	P27338-1
MAOB	ENST00000487544.1 linkuse as main transcript	n.728A>G		non_coding_transcript_exon_variant	6/7	5

Frequencies

GnomAD3 genomes

AF:

0.00237

AC:

267

AN:

112604

Hom.:

Cov.:

AF XY:

0.00193

AC XY:

AN XY:

34766

show subpopulations

Gnomad AFR

AF:

0.000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000563

Gnomad ASJ

AF:

0.000378

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000803

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00443

Gnomad OTH

AF:

0.00262

GnomAD3 exomes

AF:

0.00185

AC:

322

AN:

174085

Hom.:

AF XY:

0.00178

AC XY:

106

AN XY:

59555

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.000337

Gnomad ASJ exome

AF:

0.000822

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000172

Gnomad FIN exome

AF:

0.00144

Gnomad NFE exome

AF:

0.00350

Gnomad OTH exome

AF:

0.00139

GnomAD4 exome

AF:

0.00307

AC:

3321

AN:

1081737

Hom.:

Cov.:

AF XY:

0.00305

AC XY:

1062

AN XY:

348105

show subpopulations

Gnomad4 AFR exome

AF:

0.000268

Gnomad4 AMR exome

AF:

0.000344

Gnomad4 ASJ exome

AF:

0.000937

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000208

Gnomad4 FIN exome

AF:

0.00137

Gnomad4 NFE exome

AF:

0.00374

Gnomad4 OTH exome

AF:

0.00242

GnomAD4 genome

AF:

0.00237

AC:

267

AN:

112658

Hom.:

Cov.:

AF XY:

0.00195

AC XY:

AN XY:

34830

show subpopulations

Gnomad4 AFR

AF:

0.000482

Gnomad4 AMR

AF:

0.000563

Gnomad4 ASJ

AF:

0.000378

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000803

Gnomad4 NFE

AF:

0.00443

Gnomad4 OTH

AF:

0.00259

Alfa

AF:

0.00400

Hom.:

Bravo

AF:

0.00210

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 18, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

1.2

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over