rs6520901

Variant names:

• chrX-43793719-C-G
• rs6520901
• NM_000898.5:c.769-141G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_000898.5(MAOB):​c.769-141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 468,123 control chromosomes in the GnomAD database, including 3 homozygotes. There are 144 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 0.0036 (2 hom., 117 hem., cov: 23)
  • Exomes 𝑓: 0.00042 (1 hom. 27 hem.)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 1 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.769-141G>C		intron_variant	Intron 7 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.721-141G>C		intron_variant	Intron 7 of 14		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.769-141G>C		intron_variant	Intron 7 of 14	1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.00353 AC: 394 AN: 111665 Hom.: 2 Cov.: 23

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00218

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000941

Gnomad OTH AF: 0.00133

GnomAD4 exome AF: 0.000421 AC: 150 AN: 356408 Hom.: 1 AF XY: 0.000289 AC XY: 27 AN XY: 93310

African (AFR) AF: 0.0128 AC: 109 AN: 8518

American (AMR) AF: 0.00118 AC: 12 AN: 10143

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9887

East Asian (EAS) AF: 0.00 AC: 0 AN: 19995

South Asian (SAS) AF: 0.00 AC: 0 AN: 21107

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31272

Middle Eastern (MID) AF: 0.00184 AC: 3 AN: 1633

European-Non Finnish (NFE) AF: 0.00000855 AC: 2 AN: 233823

Other (OTH) AF: 0.00120 AC: 24 AN: 20030

GnomAD4 genome AF: 0.00361 AC: 403 AN: 111715 Hom.: 2 Cov.: 23 AF XY: 0.00345 AC XY: 117 AN XY: 33925

African (AFR) AF: 0.0121 AC: 373 AN: 30721

American (AMR) AF: 0.00218 AC: 23 AN: 10545

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2647

East Asian (EAS) AF: 0.00 AC: 0 AN: 3529

South Asian (SAS) AF: 0.00 AC: 0 AN: 2621

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6100

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 219

European-Non Finnish (NFE) AF: 0.0000941 AC: 5 AN: 53124

Other (OTH) AF: 0.00131 AC: 2 AN: 1522

Alfa AF: 0.00256 Hom.: 4

Bravo AF: 0.00402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.054
DANN	Benign	0.47
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism

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: rs6520901; hg19: chrX-43652966;