chrX-43855938-G-A

Variant names:

• chrX-43855938-G-A
• rs2239441
• NM_000898.5:c.47-12174C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000898.5(MAOB):​c.47-12174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 110,990 control chromosomes in the GnomAD database, including 554 homozygotes. There are 2,305 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 0.072 (554 hom., 2305 hem., cov: 22)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

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.47-12174C>T		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.47-12174C>T		intron	N/A	ENSP00000367309.4
	MAOB	ENST00000468431.1	TSL:3	n.51-11293C>T		intron	N/A
	MAOB	ENST00000487544.1	TSL:5	n.183-11293C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 8013 AN: 110940 Hom.: 554 Cov.: 22

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.00134

Gnomad MID AF: 0.00851

Gnomad NFE AF: 0.00372

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0724 AC: 8036 AN: 110990 Hom.: 554 Cov.: 22 AF XY: 0.0693 AC XY: 2305 AN XY: 33270

African (AFR) AF: 0.215 AC: 6529 AN: 30367

American (AMR) AF: 0.0327 AC: 343 AN: 10474

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 42 AN: 2642

East Asian (EAS) AF: 0.0995 AC: 350 AN: 3517

South Asian (SAS) AF: 0.170 AC: 441 AN: 2599

European-Finnish (FIN) AF: 0.00134 AC: 8 AN: 5982

Middle Eastern (MID) AF: 0.00935 AC: 2 AN: 214

European-Non Finnish (NFE) AF: 0.00372 AC: 197 AN: 52995

Other (OTH) AF: 0.0816 AC: 124 AN: 1520

Alfa AF: 0.0330 Hom.: 3253

Bravo AF: 0.0802

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.036
DANN	Benign	0.71
PhyloP100		-1.0
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: rs2239441; hg19: chrX-43715184;