rs4824562

chrX-43844544-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.47-780A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 111,444 control chromosomes in the GnomAD database, including 739 homozygotes. There are 4,148 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 0.12 (739 hom., 4141 hem., cov: 23)
  • Exomes 𝑓: 0.34 (0 hom. 7 hem.)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5	c.47-780A>G		intron_variant		ENST00000378069.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5	c.47-780A>G		intron_variant		1	NM_000898.5	P1
MAOB	ENST00000468431.1	n.152A>G		non_coding_transcript_exon_variant	2/3	3
MAOB	ENST00000487544.1	n.284A>G		non_coding_transcript_exon_variant	2/7	5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 13839 AN: 111364 Hom.: 738 Cov.: 23 AF XY: 0.123 AC XY: 4138 AN XY: 33566

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0502

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.345 AC: 10 AN: 29 Hom.: 0 Cov.: 0 AF XY: 0.467 AC XY: 7 AN XY: 15

Gnomad4 AMR exome AF: 1.00

Gnomad4 NFE exome AF: 0.321

GnomAD4 genome AF: 0.124 AC: 13839 AN: 111415 Hom.: 739 Cov.: 23 AF XY: 0.123 AC XY: 4141 AN XY: 33627

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.121

Alfa AF: 0.152 Hom.: 5135

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.8
Dann	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs4824562; hg19: chrX-43703790; COSMIC: COSV65207213;