rs6651806

Variant names:

• chrX-43829718-A-C
• rs6651806
• NM_000898.5:c.279+9150T>G

Your query was ambiguous. Multiple possible variants found:

• chrX-43829718-A-C
• chrX-43829718-A-G
• chrX-43829718-A-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.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
• Publications: 16 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=-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 rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.279+9150T>G		intron_variant	Intron 3 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.231+9150T>G		intron_variant	Intron 3 of 14		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.279+9150T>G		intron_variant	Intron 3 of 14	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000487544.1	n.605+9150T>G		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.369 AC: 41093 AN: 111233 Hom.: 6698 Cov.: 23

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

African (AFR) AF: 0.626 AC: 19061 AN: 30470

American (AMR) AF: 0.223 AC: 2345 AN: 10521

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 829 AN: 2638

East Asian (EAS) AF: 0.121 AC: 429 AN: 3546

South Asian (SAS) AF: 0.277 AC: 737 AN: 2658

European-Finnish (FIN) AF: 0.231 AC: 1393 AN: 6033

Middle Eastern (MID) AF: 0.470 AC: 101 AN: 215

European-Non Finnish (NFE) AF: 0.295 AC: 15615 AN: 52999

Other (OTH) AF: 0.369 AC: 564 AN: 1527

Alfa AF: 0.309 Hom.: 17354

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
PhyloP100		-0.68
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: rs6651806; hg19: chrX-43688964;