NM_000898.5:c.280-4697T>C

Variant names:

• chrX-43808101-A-G
• rs1014876
• NM_000898.5:c.280-4697T>C

Variant summary

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

The NM_000898.5(MAOB):​c.280-4697T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0195 in 111,002 control chromosomes in the GnomAD database, including 60 homozygotes. There are 650 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 0.020 (60 hom., 650 hem., cov: 23)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	NM_000898.5	MANE Select	c.280-4697T>C		intron	N/A	NP_000889.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	ENST00000378069.5	TSL:1 MANE Select	c.280-4697T>C		intron	N/A	ENSP00000367309.4	P27338-1
	MAOB	ENST00000890313.1		c.280-4697T>C		intron	N/A	ENSP00000560372.1
	MAOB	ENST00000890309.1		c.280-4697T>C		intron	N/A	ENSP00000560368.1

Frequencies

GnomAD3 genomes AF: 0.0194 AC: 2156 AN: 110953 Hom.: 57 Cov.: 23

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00954

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.00168

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00317

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0195 AC: 2165 AN: 111002 Hom.: 60 Cov.: 23 AF XY: 0.0196 AC XY: 650 AN XY: 33186

African (AFR) AF: 0.0332 AC: 1011 AN: 30455

American (AMR) AF: 0.00953 AC: 100 AN: 10492

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 42 AN: 2640

East Asian (EAS) AF: 0.101 AC: 352 AN: 3475

South Asian (SAS) AF: 0.175 AC: 440 AN: 2519

European-Finnish (FIN) AF: 0.00168 AC: 10 AN: 5964

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 217

European-Non Finnish (NFE) AF: 0.00317 AC: 168 AN: 53050

Other (OTH) AF: 0.0279 AC: 42 AN: 1507

Alfa AF: 0.0121 Hom.: 61

Bravo AF: 0.0197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.10
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: rs1014876; hg19: chrX-43667348;