rs56220155

chrX-43773915-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000898.5(MAOB):c.1235+1260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 110,876 control chromosomes in the GnomAD database, including 3,914 homozygotes. There are 9,487 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 0.30 (3914 hom., 9487 hem., cov: 22)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5	c.1235+1260A>G		intron_variant		ENST00000378069.5
MAOB	XM_017029524.3	c.1187+1260A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5	c.1235+1260A>G		intron_variant		1	NM_000898.5	P1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 33181 AN: 110824 Hom.: 3912 Cov.: 22 AF XY: 0.286 AC XY: 9461 AN XY: 33068

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.299 AC: 33207 AN: 110876 Hom.: 3914 Cov.: 22 AF XY: 0.286 AC XY: 9487 AN XY: 33130

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.317

Alfa AF: 0.286 Hom.: 1785

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21
Dann	Benign	0.41

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: rs56220155; hg19: chrX-43633162;