rs6651806

Positions:

• chrX-43829718-A-C
• chrX-43829718-A-G
• chrX-43829718-A-T

Variant summary

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

The NM_000898.5(MAOB):​c.279+9150T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 111,289 control chromosomes in the GnomAD database, including 6,700 homozygotes. There are 11,719 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 0.37 (6700 hom., 11719 hem., cov: 23)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5	c.279+9150T>G		intron_variant		ENST00000378069.5
MAOB	XM_017029524.3	c.231+9150T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5	c.279+9150T>G		intron_variant		1	NM_000898.5	P1
MAOB	ENST00000487544.1	n.605+9150T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.369 AC: 41093 AN: 111233 Hom.: 6698 Cov.: 23 AF XY: 0.349 AC XY: 11688 AN XY: 33469

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.0777

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.370 AC: 41127 AN: 111289 Hom.: 6700 Cov.: 23 AF XY: 0.349 AC XY: 11719 AN XY: 33535

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.369

Alfa AF: 0.291 Hom.: 12130

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.33

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: rs6651806; hg19: chrX-43688964;