dbSNP rs17462: MAOB:c.*217A>G (chrX-43767249-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000898.5(MAOB):c.*217A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0243 in 352,407 control chromosomes in the GnomAD database, including 585 homozygotes. There are 2,214 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 0.058 ( 462 hom., 1708 hem., cov: 22)

Exomes 𝑓: 0.0087 ( 123 hom. 506 hem. )

Consequence

MAOB
NM_000898.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.529

Publications

4 publications found

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 -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5 link	c.*217A>G		3_prime_UTR_variant	Exon 15 of 15	ENST00000378069.5	NP_000889.3	P27338-1
MAOB	XM_017029524.3 link	c.*217A>G		3_prime_UTR_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.*217A>G		3_prime_UTR_variant	Exon 15 of 15	1	NM_000898.5	ENSP00000367309.4		P27338-1

Frequencies

GnomAD3 genomes

AF:

0.0581

AC:

6464

AN:

111305

Hom.:

461

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0256

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00112

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0294

Gnomad NFE

AF:

0.000697

Gnomad OTH

AF:

0.0447

GnomAD4 exome

AF:

0.00866

AC:

2088

AN:

241048

Hom.:

123

Cov.:

AF XY:

0.00736

AC XY:

506

AN XY:

68766

show subpopulations

African (AFR)

AF:

0.201

AC:

1532

AN:

7633

American (AMR)

AF:

0.0169

AC:

158

AN:

9376

Ashkenazi Jewish (ASJ)

AF:

0.000254

AC:

AN:

7883

East Asian (EAS)

AF:

0.00

AC:

AN:

19518

South Asian (SAS)

AF:

0.000257

AC:

AN:

7780

European-Finnish (FIN)

AF:

0.0000542

AC:

AN:

18456

Middle Eastern (MID)

AF:

0.00997

AC:

AN:

1103

European-Non Finnish (NFE)

AF:

0.000520

AC:

AN:

153724

Other (OTH)

AF:

0.0194

AC:

302

AN:

15575

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

132

197

263

329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<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:

0.0582

AC:

6477

AN:

111359

Hom.:

462

Cov.:

AF XY:

0.0509

AC XY:

1708

AN XY:

33573

show subpopulations

African (AFR)

AF:

0.200

AC:

6095

AN:

30454

American (AMR)

AF:

0.0255

AC:

268

AN:

10507

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2652

East Asian (EAS)

AF:

0.00

AC:

AN:

3533

South Asian (SAS)

AF:

0.00112

AC:

AN:

2671

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6051

Middle Eastern (MID)

AF:

0.0323

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.000697

AC:

AN:

53069

Other (OTH)

AF:

0.0441

AC:

AN:

1518

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

189

378

566

755

944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0326

Hom.:

2184

Bravo

AF:

0.0685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.53

(source)

DANN

Benign

0.42

PhyloP100

-0.53

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over