rs2283728

Variant names:

• chrX-43773881-G-A
• rs2283728
• NM_000898.5:c.1235+1294C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-43773881-G-A
• chrX-43773881-G-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+1294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 111,445 control chromosomes in the GnomAD database, including 318 homozygotes. There are 1,714 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 0.052 (318 hom., 1714 hem., cov: 23)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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 (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1235+1294C>T		intron_variant	Intron 12 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1187+1294C>T		intron_variant	Intron 12 of 14		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.1235+1294C>T		intron_variant	Intron 12 of 14	1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 5805 AN: 111393 Hom.: 315 Cov.: 23 AF XY: 0.0506 AC XY: 1700 AN XY: 33593

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0201

Gnomad EAS AF: 0.0999

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.000663

Gnomad MID AF: 0.00418

Gnomad NFE AF: 0.00356

Gnomad OTH AF: 0.0486

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

GnomAD4 genome AF: 0.0523 AC: 5829 AN: 111445 Hom.: 318 Cov.: 23 AF XY: 0.0509 AC XY: 1714 AN XY: 33655

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.0201

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.000663

Gnomad4 NFE AF: 0.00356

Gnomad4 OTH AF: 0.0579

Alfa AF: 0.00274 Hom.: 35

Bravo AF: 0.0569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.26

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: rs2283728; hg19: chrX-43633128;