dbSNP rs3027459: MAOB:c.476+142G>A (chrX-43802030-C-T) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.397

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:

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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=-0.88).

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 link	c.476+142G>A		intron_variant	Intron 5 of 14	ENST00000378069.5	NP_000889.3	P27338-1
MAOB	XM_017029524.3 link	c.428+142G>A		intron_variant	Intron 5 of 14		XP_016885013.1	B7Z242

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5 link	c.476+142G>A		intron_variant	Intron 5 of 14	1	NM_000898.5	ENSP00000367309.4		P27338-1
MAOB	ENST00000487544.1 link	n.802+142G>A		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.0162

AC:

1829

AN:

112826

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.00164

AC XY:

223

AN XY:

135967

show subpopulations

African (AFR)

AF:

0.0569

AC:

706

AN:

12407

American (AMR)

AF:

0.00311

AC:

AN:

25069

Ashkenazi Jewish (ASJ)

AF:

0.0000761

AC:

AN:

13148

East Asian (EAS)

AF:

0.00

AC:

AN:

23832

South Asian (SAS)

AF:

0.0000894

AC:

AN:

33547

European-Finnish (FIN)

AF:

0.0000377

AC:

AN:

26492

Middle Eastern (MID)

AF:

0.00281

AC:

AN:

2851

European-Non Finnish (NFE)

AF:

0.000133

AC:

AN:

240088

Other (OTH)

AF:

0.00412

AC:

AN:

22793

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

107

142

178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0162

AC:

1833

AN:

112877

Hom.:

Cov.:

AF XY:

0.0140

AC XY:

490

AN XY:

35039

show subpopulations

African (AFR)

AF:

0.0558

AC:

1736

AN:

31120

American (AMR)

AF:

0.00616

AC:

AN:

10710

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2653

East Asian (EAS)

AF:

0.00

AC:

AN:

3579

South Asian (SAS)

AF:

0.00

AC:

AN:

2765

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6291

Middle Eastern (MID)

AF:

0.00461

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.000150

AC:

AN:

53314

Other (OTH)

AF:

0.0143

AC:

AN:

1541

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

123

185

246

308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00492

Hom.:

130

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

(source)

DANN

Benign

0.42

PhyloP100

-0.40

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

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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