chrX-43867148-A-G

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.46+15106T>C		intron_variant	Intron 1 of 14	ENST00000378069.5	NP_000889.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.46+15106T>C		intron_variant	Intron 1 of 14	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000468431.1	n.50+15106T>C		intron_variant	Intron 1 of 2	3
MAOB	ENST00000487544.1	n.182+15106T>C		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.593 AC: 65525 AN: 110440 Hom.: 15415 Cov.: 23 AF XY: 0.575 AC XY: 18784 AN XY: 32668

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

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.576

Alfa AF: 0.509 Hom.: 23617

Bravo AF: 0.605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.51

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: rs5905512; hg19: chrX-43726394;