X-43870877-T-C

Position:

• chrX-43870877-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000898.5(MAOB):​c.46+11377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 108,701 control chromosomes in the GnomAD database, including 378 homozygotes. There are 1,559 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 (378 hom., 1559 hem., cov: 21)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5	c.46+11377A>G		intron_variant		ENST00000378069.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5	c.46+11377A>G		intron_variant		1	NM_000898.5	P1
MAOB	ENST00000468431.1	n.50+11377A>G		intron_variant, non_coding_transcript_variant		3
MAOB	ENST00000487544.1	n.182+11377A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0582 AC: 6324 AN: 108668 Hom.: 378 Cov.: 21 AF XY: 0.0496 AC XY: 1546 AN XY: 31200

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.00159

Gnomad MID AF: 0.00433

Gnomad NFE AF: 0.00361

Gnomad OTH AF: 0.0626

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0583 AC: 6336 AN: 108701 Hom.: 378 Cov.: 21 AF XY: 0.0499 AC XY: 1559 AN XY: 31241

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0876

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.00159

Gnomad4 NFE AF: 0.00361

Gnomad4 OTH AF: 0.0707

Alfa AF: 0.0157 Hom.: 479

Bravo AF: 0.0664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.42

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

LitVar

Other links and lift over

dbSNP: rs9887047; hg19: chrX-43730123;