dbSNP rs3027440: MAOB:c.*232T>C (chrX-43767234-A-G) – 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.*232T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 345,095 control chromosomes in the GnomAD database, including 405 homozygotes. There are 2,804 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 ( 100 hom., 965 hem., cov: 23)

Exomes 𝑓: 0.027 ( 305 hom. 1839 hem. )

Consequence

MAOB
NM_000898.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5 link	c.*232T>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000378069.5	NP_000889.3	P27338-1
MAOB	XM_017029524.3 link	c.*232T>C		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.*232T>C		3_prime_UTR_variant	Exon 15 of 15	1	NM_000898.5	ENSP00000367309.4		P27338-1

Frequencies

GnomAD3 genomes

AF:

0.0275

AC:

3071

AN:

111509

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0355

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0666

Gnomad ASJ

AF:

0.0215

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.00247

Gnomad MID

AF:

0.00420

Gnomad NFE

AF:

0.00337

Gnomad OTH

AF:

0.0254

GnomAD4 exome

AF:

0.0265

AC:

6191

AN:

233527

Hom.:

305

Cov.:

AF XY:

0.0282

AC XY:

1839

AN XY:

65299

show subpopulations

African (AFR)

AF:

0.0339

AC:

259

AN:

7635

American (AMR)

AF:

0.0655

AC:

602

AN:

9189

Ashkenazi Jewish (ASJ)

AF:

0.0149

AC:

116

AN:

7775

East Asian (EAS)

AF:

0.160

AC:

3058

AN:

19137

South Asian (SAS)

AF:

0.155

AC:

1202

AN:

7777

European-Finnish (FIN)

AF:

0.00335

AC:

AN:

17930

Middle Eastern (MID)

AF:

0.00837

AC:

AN:

1075

European-Non Finnish (NFE)

AF:

0.00335

AC:

495

AN:

147755

Other (OTH)

AF:

0.0256

AC:

390

AN:

15254

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

166

333

499

666

832

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0276

AC:

3078

AN:

111568

Hom.:

100

Cov.:

AF XY:

0.0286

AC XY:

965

AN XY:

33758

show subpopulations

African (AFR)

AF:

0.0354

AC:

1086

AN:

30668

American (AMR)

AF:

0.0662

AC:

696

AN:

10509

Ashkenazi Jewish (ASJ)

AF:

0.0215

AC:

AN:

2649

East Asian (EAS)

AF:

0.148

AC:

515

AN:

3491

South Asian (SAS)

AF:

0.182

AC:

477

AN:

2625

European-Finnish (FIN)

AF:

0.00247

AC:

AN:

6079

Middle Eastern (MID)

AF:

0.00

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.00337

AC:

179

AN:

53134

Other (OTH)

AF:

0.0350

AC:

AN:

1516

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

192

288

384

480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0148

Hom.:

1001

Bravo

AF:

0.0323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.3

(source)

DANN

Benign

0.43

PhyloP100

1.0

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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rs3027440

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