dbSNP rs6324: MAOB:p.Pro487Pro (chrX-43767568-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000898.5(MAOB):c.1461C>T(p.Pro487Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 1,208,570 control chromosomes in the GnomAD database, including 1,005 homozygotes. There are 10,534 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 0.028 ( 102 hom., 983 hem., cov: 22)

Exomes 𝑓: 0.021 ( 903 hom. 9551 hem. )

Consequence

MAOB
NM_000898.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.506

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 was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP7

Synonymous conserved (PhyloP=0.506 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5 link	c.1461C>T	p.Pro487Pro	synonymous_variant	Exon 15 of 15	ENST00000378069.5	NP_000889.3	P27338-1
MAOB	XM_017029524.3 link	c.1413C>T	p.Pro471Pro	synonymous_variant	Exon 15 of 15		XP_016885013.1	B7Z242

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5 link	c.1461C>T	p.Pro487Pro	synonymous_variant	Exon 15 of 15	1	NM_000898.5	ENSP00000367309.4		P27338-1

Frequencies

GnomAD3 genomes

AF:

0.0276

AC:

3085

AN:

111629

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0356

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0675

Gnomad ASJ

AF:

0.0212

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.00262

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.00333

Gnomad OTH

AF:

0.0279

GnomAD2 exomes

AF:

0.0500

AC:

9118

AN:

182202

AF XY:

0.0544

show subpopulations

Gnomad AFR exome

AF:

0.0391

Gnomad AMR exome

AF:

0.0903

Gnomad ASJ exome

AF:

0.0167

Gnomad EAS exome

AF:

0.145

Gnomad FIN exome

AF:

0.00307

Gnomad NFE exome

AF:

0.00316

Gnomad OTH exome

AF:

0.0335

GnomAD4 exome

AF:

0.0206

AC:

22599

AN:

1096885

Hom.:

903

Cov.:

AF XY:

0.0264

AC XY:

9551

AN XY:

362399

show subpopulations

Gnomad4 AFR exome

AF:

0.0363

AC:

956

AN:

26372

Gnomad4 AMR exome

AF:

0.0877

AC:

3080

AN:

35134

Gnomad4 ASJ exome

AF:

0.0170

AC:

330

AN:

19368

Gnomad4 EAS exome

AF:

0.160

AC:

4840

AN:

30170

Gnomad4 SAS exome

AF:

0.181

AC:

9792

AN:

53997

Gnomad4 FIN exome

AF:

0.00343

AC:

139

AN:

40507

Gnomad4 NFE exome

AF:

0.00240

AC:

2016

AN:

841428

Gnomad4 Remaining exome

AF:

0.0303

AC:

1394

AN:

46012

Heterozygous variant carriers

600

1200

1800

2400

3000

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

350

700

1050

1400

1750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0277

AC:

3093

AN:

111685

Hom.:

102

Cov.:

AF XY:

0.0290

AC XY:

983

AN XY:

33855

show subpopulations

Gnomad4 AFR

AF:

0.0356

AC:

0.0355678

AN:

0.0355678

Gnomad4 AMR

AF:

0.0671

AC:

0.0671415

AN:

0.0671415

Gnomad4 ASJ

AF:

0.0212

AC:

0.021156

AN:

0.021156

Gnomad4 EAS

AF:

0.149

AC:

0.149386

AN:

0.149386

Gnomad4 SAS

AF:

0.178

AC:

0.178462

AN:

0.178462

Gnomad4 FIN

AF:

0.00262

AC:

0.00262467

AN:

0.00262467

Gnomad4 NFE

AF:

0.00333

AC:

0.00332995

AN:

0.00332995

Gnomad4 OTH

AF:

0.0374

AC:

0.0374016

AN:

0.0374016

Heterozygous variant carriers

192

289

385

481

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

114

152

190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0137

Hom.:

1176

Bravo

AF:

0.0323

EpiCase

AF:

0.00421

EpiControl

AF:

0.00250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

3.1

DANN

Benign

0.60

Mutation Taster

=98/2

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

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