Variant chrX-43768646-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_000898.5(MAOB):c.1410+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00282 in 1,193,371 control chromosomes in the GnomAD database, including 54 homozygotes. There are 907 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 29 hom., 444 hem., cov: 22)

Exomes 𝑓: 0.0016 ( 25 hom. 463 hem. )

Consequence

MAOB
NM_000898.5 splice_region, intron

Scores

Splicing: ADA: 0.0004028

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.325

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant X-43768646-T-C is Benign according to our data. Variant chrX-43768646-T-C is described in ClinVar as [Benign]. Clinvar id is 791380.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (1612/111862) while in subpopulation AFR AF= 0.0498 (1532/30751). AF 95% confidence interval is 0.0477. There are 29 homozygotes in gnomad4. There are 444 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 29 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5 linkuse as main transcript	c.1410+8A>G		splice_region_variant, intron_variant		ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3 linkuse as main transcript	c.1362+8A>G		splice_region_variant, intron_variant			XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5 linkuse as main transcript	c.1410+8A>G		splice_region_variant, intron_variant		1	NM_000898.5	ENSP00000367309	P1	P27338-1

Frequencies

GnomAD3 genomes

AF:

0.0144

AC:

1614

AN:

111807

Hom.:

Cov.:

AF XY:

0.0130

AC XY:

441

AN XY:

33999

show subpopulations

Gnomad AFR

AF:

0.0500

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00447

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000281

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000263

Gnomad OTH

AF:

0.0119

GnomAD3 exomes

AF:

0.00436

AC:

794

AN:

182181

Hom.:

AF XY:

0.00322

AC XY:

215

AN XY:

66859

show subpopulations

Gnomad AFR exome

AF:

0.0527

Gnomad AMR exome

AF:

0.00282

Gnomad ASJ exome

AF:

0.000134

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000106

Gnomad FIN exome

AF:

0.000125

Gnomad NFE exome

AF:

0.000172

Gnomad OTH exome

AF:

0.00178

GnomAD4 exome

AF:

0.00162

AC:

1757

AN:

1081509

Hom.:

Cov.:

AF XY:

0.00133

AC XY:

463

AN XY:

348609

show subpopulations

Gnomad4 AFR exome

AF:

0.0492

Gnomad4 AMR exome

AF:

0.00319

Gnomad4 ASJ exome

AF:

0.0000520

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000112

Gnomad4 FIN exome

AF:

0.0000742

Gnomad4 NFE exome

AF:

0.000210

Gnomad4 OTH exome

AF:

0.00367

GnomAD4 genome

AF:

0.0144

AC:

1612

AN:

111862

Hom.:

Cov.:

AF XY:

0.0130

AC XY:

444

AN XY:

34064

show subpopulations

Gnomad4 AFR

AF:

0.0498

Gnomad4 AMR

AF:

0.00446

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000282

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000263

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.0126

Hom.:

Bravo

AF:

0.0172

EpiCase

AF:

0.000110

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.8

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00040

dbscSNV1_RF

Benign

0.036

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over