X-43773881-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.97).
• 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 the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• 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

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

African (AFR) AF: 0.00712 AC: 218 AN: 30603

American (AMR) AF: 0.0301 AC: 317 AN: 10536

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 261 AN: 2634

East Asian (EAS) AF: 0.000284 AC: 1 AN: 3515

South Asian (SAS) AF: 0.0166 AC: 44 AN: 2645

European-Finnish (FIN) AF: 0.0350 AC: 211 AN: 6035

Middle Eastern (MID) AF: 0.0826 AC: 18 AN: 218

European-Non Finnish (NFE) AF: 0.0454 AC: 2410 AN: 53071

Other (OTH) AF: 0.0408 AC: 62 AN: 1520

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
PhyloP100		-0.54
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: rs2283728; hg19: chrX-43633128;