X-43773915-T-C

Variant names:

• chrX-43773915-T-C
• rs56220155
• NM_000898.5:c.1235+1260A>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+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
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 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+1260A>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+1260A>G		intron	N/A	ENSP00000367309.4
	MAOB	ENST00000890313.1		c.1340+1260A>G		intron	N/A	ENSP00000560372.1
	MAOB	ENST00000890309.1		c.1235+1260A>G		intron	N/A	ENSP00000560368.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 33181 AN: 110824 Hom.: 3912 Cov.: 22

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

African (AFR) AF: 0.403 AC: 12258 AN: 30391

American (AMR) AF: 0.189 AC: 1971 AN: 10452

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 831 AN: 2632

East Asian (EAS) AF: 0.121 AC: 425 AN: 3508

South Asian (SAS) AF: 0.273 AC: 720 AN: 2639

European-Finnish (FIN) AF: 0.233 AC: 1383 AN: 5937

Middle Eastern (MID) AF: 0.410 AC: 89 AN: 217

European-Non Finnish (NFE) AF: 0.283 AC: 14995 AN: 52899

Other (OTH) AF: 0.317 AC: 480 AN: 1515

Alfa AF: 0.286 Hom.: 1785

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.41
PhyloP100		-1.8
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: rs56220155; hg19: chrX-43633162;