X-43792264-A-T

Variant names:

• chrX-43792264-A-T
• rs2311013
• NM_000898.5:c.928+1155T>A

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000898.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	NM_000898.5	MANE Select	c.928+1155T>A		intron	N/A	NP_000889.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	ENST00000378069.5	TSL:1 MANE Select	c.928+1155T>A		intron	N/A	ENSP00000367309.4
	MAOB	ENST00000890313.1		c.1033+955T>A		intron	N/A	ENSP00000560372.1
	MAOB	ENST00000890309.1		c.928+1155T>A		intron	N/A	ENSP00000560368.1

Frequencies

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

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

African (AFR) AF: 0.993 AC: 30392 AN: 30598

American (AMR) AF: 0.973 AC: 10091 AN: 10369

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 2590 AN: 2645

East Asian (EAS) AF: 1.00 AC: 3549 AN: 3550

South Asian (SAS) AF: 0.979 AC: 2585 AN: 2641

European-Finnish (FIN) AF: 0.954 AC: 5615 AN: 5887

Middle Eastern (MID) AF: 0.995 AC: 216 AN: 217

European-Non Finnish (NFE) AF: 0.954 AC: 50665 AN: 53127

Other (OTH) AF: 0.973 AC: 1468 AN: 1508

Alfa AF: 0.934 Hom.: 3746

Bravo AF: 0.972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.031
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2311013; hg19: chrX-43651511;