rs7883073

Positions:

• chrX-43838294-T-C
• chrX-43838294-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000378069.5(MAOB):​c.279+574A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 111,412 control chromosomes in the GnomAD database, including 122 homozygotes. There are 1,038 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 0.031 (122 hom., 1038 hem., cov: 23)
• Consequence: MAOB ENST00000378069.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.279+574A>G		intron_variant		ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.231+574A>G		intron_variant			XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.279+574A>G		intron_variant		1	NM_000898.5	ENSP00000367309	P1
MAOB	ENST00000487544.1	n.605+574A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 3414 AN: 111358 Hom.: 119 Cov.: 23 AF XY: 0.0306 AC XY: 1027 AN XY: 33576

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00916

Gnomad ASJ AF: 0.0152

Gnomad EAS AF: 0.0987

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.00150

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00267

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0308 AC: 3436 AN: 111412 Hom.: 122 Cov.: 23 AF XY: 0.0309 AC XY: 1038 AN XY: 33640

Gnomad4 AFR AF: 0.0750

Gnomad4 AMR AF: 0.00905

Gnomad4 ASJ AF: 0.0152

Gnomad4 EAS AF: 0.0990

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.00150

Gnomad4 NFE AF: 0.00267

Gnomad4 OTH AF: 0.0330

Alfa AF: 0.0128 Hom.: 540

Bravo AF: 0.0315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.74

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: rs7883073; hg19: chrX-43697540;