rs7888450

Positions:

• chrX-43774756-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+419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 111,841 control chromosomes in the GnomAD database, including 429 homozygotes. There are 1,928 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 0.060 (429 hom., 1928 hem., cov: 23)
• Consequence: MAOB NM_000898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOB	NM_000898.5	c.1235+419A>G		intron_variant		ENST00000378069.5
MAOB	XM_017029524.3	c.1187+419A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOB	ENST00000378069.5	c.1235+419A>G		intron_variant		1	NM_000898.5	P1

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 6719 AN: 111789 Hom.: 427 Cov.: 23 AF XY: 0.0562 AC XY: 1910 AN XY: 33973

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.000489

Gnomad MID AF: 0.00418

Gnomad NFE AF: 0.00342

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0603 AC: 6746 AN: 111841 Hom.: 429 Cov.: 23 AF XY: 0.0566 AC XY: 1928 AN XY: 34035

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.0872

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.000489

Gnomad4 NFE AF: 0.00342

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0147 Hom.: 356

Bravo AF: 0.0654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.096
DANN	Benign	0.49

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: rs7888450; hg19: chrX-43634003;