X-43773881-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000898.5(MAOB):​c.1235+1294C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 111,463 control chromosomes in the GnomAD database, including 60 homozygotes. There are 1,005 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 0.032 (60 hom., 1005 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=-0.97).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.032 (3562/111463) while in subpopulation NFE AF= 0.0454 (2410/53071). AF 95% confidence interval is 0.0439. There are 60 homozygotes in gnomad4. There are 1005 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 60 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.1235+1294C>G		intron_variant	Intron 12 of 14	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.1187+1294C>G		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>G		intron_variant	Intron 12 of 14	1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 3563 AN: 111411 Hom.: 60 Cov.: 23 AF XY: 0.0299 AC XY: 1005 AN XY: 33601

Gnomad AFR AF: 0.00714

Gnomad AMI AF: 0.0292

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.000284

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0753

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0413

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

GnomAD4 genome AF: 0.0320 AC: 3562 AN: 111463 Hom.: 60 Cov.: 23 AF XY: 0.0299 AC XY: 1005 AN XY: 33663

Gnomad4 AFR AF: 0.00712

Gnomad4 AMR AF: 0.0301

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.000284

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0350

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0408

Alfa AF: 0.00910 Hom.: 35

Bravo AF: 0.0309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.24

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;