NM_000898.5:c.46+15106T>C

Variant names:

• chrX-43867148-A-G
• rs5905512
• NM_000898.5:c.46+15106T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000898.5(MAOB):​c.46+15106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.59 (15417 hom., 18834 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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.46+15106T>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.46+15106T>C		intron	N/A	ENSP00000367309.4	P27338-1
	MAOB	ENST00000890313.1		c.46+15106T>C		intron	N/A	ENSP00000560372.1
	MAOB	ENST00000890309.1		c.46+15106T>C		intron	N/A	ENSP00000560368.1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 65525 AN: 110440 Hom.: 15415 Cov.: 23

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.574

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.593 AC: 65577 AN: 110493 Hom.: 15417 Cov.: 23 AF XY: 0.575 AC XY: 18834 AN XY: 32731

African (AFR) AF: 0.885 AC: 26799 AN: 30295

American (AMR) AF: 0.456 AC: 4743 AN: 10410

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1314 AN: 2638

East Asian (EAS) AF: 0.263 AC: 916 AN: 3484

South Asian (SAS) AF: 0.510 AC: 1330 AN: 2606

European-Finnish (FIN) AF: 0.430 AC: 2518 AN: 5852

Middle Eastern (MID) AF: 0.586 AC: 126 AN: 215

European-Non Finnish (NFE) AF: 0.505 AC: 26673 AN: 52809

Other (OTH) AF: 0.576 AC: 868 AN: 1508

Alfa AF: 0.536 Hom.: 39301

Bravo AF: 0.605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.51
PhyloP100		-0.46
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: rs5905512; hg19: chrX-43726394;