rs2239441

Positions:

• chrX-43855938-G-A

Variant summary

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

The ENST00000378069.5(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 ENST00000378069.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.47-12174C>T		intron_variant		ENST00000378069.5	NP_000889.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.47-12174C>T		intron_variant		1	NM_000898.5	ENSP00000367309	P1
MAOB	ENST00000468431.1	n.51-11293C>T		intron_variant, non_coding_transcript_variant		3
MAOB	ENST00000487544.1	n.183-11293C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 8013 AN: 110940 Hom.: 554 Cov.: 22 AF XY: 0.0688 AC XY: 2284 AN XY: 33210

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

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.00134

Gnomad4 NFE AF: 0.00372

Gnomad4 OTH AF: 0.0816

Alfa AF: 0.0164 Hom.: 1156

Bravo AF: 0.0802

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.036
DANN	Benign	0.71

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: rs2239441; hg19: chrX-43715184;