rs7888450

Variant names:

• chrX-43774756-T-C
• rs7888450
• NM_000898.5:c.1235+419A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000898.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	NM_000898.5	MANE Select	c.1235+419A>G		intron	N/A	NP_000889.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	ENST00000378069.5	TSL:1 MANE Select	c.1235+419A>G		intron	N/A	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 6719 AN: 111789 Hom.: 427 Cov.: 23

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

African (AFR) AF: 0.175 AC: 5350 AN: 30635

American (AMR) AF: 0.0248 AC: 262 AN: 10568

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 54 AN: 2653

East Asian (EAS) AF: 0.0872 AC: 308 AN: 3532

South Asian (SAS) AF: 0.181 AC: 486 AN: 2679

European-Finnish (FIN) AF: 0.000489 AC: 3 AN: 6141

Middle Eastern (MID) AF: 0.00461 AC: 1 AN: 217

European-Non Finnish (NFE) AF: 0.00342 AC: 182 AN: 53205

Other (OTH) AF: 0.0657 AC: 100 AN: 1523

Alfa AF: 0.0228 Hom.: 830

Bravo AF: 0.0654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.096
DANN	Benign	0.49
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7888450; hg19: chrX-43634003;