X-43792264-A-T

Position:

• chrX-43792264-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000898.5(MAOB):​c.928+1155T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.97 (36612 hom., 32380 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.928+1155T>A		intron_variant		ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.880+1155T>A		intron_variant			XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.928+1155T>A		intron_variant		1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.970 AC: 107795 AN: 111171 Hom.: 36616 Cov.: 23 AF XY: 0.970 AC XY: 32317 AN XY: 33323

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.994

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.996

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.973

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.970 AC: 107849 AN: 111224 Hom.: 36612 Cov.: 23 AF XY: 0.970 AC XY: 32380 AN XY: 33386

Gnomad4 AFR AF: 0.993

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.979

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.973

Alfa AF: 0.934 Hom.: 3746

Bravo AF: 0.972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.44

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: rs2311013; hg19: chrX-43651511;