Variant rs4824562 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000378069.5(MAOB):c.47-780A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 111,444 control chromosomes in the GnomAD database, including 739 homozygotes. There are 4,148 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 0.12 ( 739 hom., 4141 hem., cov: 23)

Exomes 𝑓: 0.34 ( 0 hom. 7 hem. )

Consequence

MAOB
ENST00000378069.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.446

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5 linkuse as main transcript	c.47-780A>G		intron_variant		ENST00000378069.5	NP_000889.3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5 linkuse as main transcript	c.47-780A>G	intron_variant		1	NM_000898.5	ENSP00000367309	P1	P27338-1
MAOB	ENST00000468431.1 linkuse as main transcript	n.152A>G	non_coding_transcript_exon_variant	2/3	3
MAOB	ENST00000487544.1 linkuse as main transcript	n.284A>G	non_coding_transcript_exon_variant	2/7	5

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

13839

AN:

111364

Hom.:

738

Cov.:

AF XY:

0.123

AC XY:

4138

AN XY:

33566

show subpopulations

Gnomad AFR

AF:

0.0315

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.0502

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.122

GnomAD4 exome

AF:

0.345

AC:

AN:

Hom.:

Cov.:

AF XY:

0.467

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.321

GnomAD4 genome

AF:

0.124

AC:

13839

AN:

111415

Hom.:

739

Cov.:

AF XY:

0.123

AC XY:

4141

AN XY:

33627

show subpopulations

Gnomad4 AFR

AF:

0.0315

Gnomad4 AMR

AF:

0.175

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.181

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.152

Hom.:

5135

Bravo

AF:

0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.8

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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