X-43767234-A-G

Position:

• chrX-43767234-A-G

Variant summary

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

The NM_000898.5(MAOB):​c.*232T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 345,095 control chromosomes in the GnomAD database, including 405 homozygotes. There are 2,804 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 0.028 (100 hom., 965 hem., cov: 23)
  • Exomes 𝑓: 0.027 (305 hom. 1839 hem.)
• Consequence: MAOB NM_000898.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOB	NM_000898.5	c.*232T>C		3_prime_UTR_variant	15/15	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.*232T>C		3_prime_UTR_variant	15/15		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069	c.*232T>C		3_prime_UTR_variant	15/15	1	NM_000898.5	ENSP00000367309.4

Frequencies

GnomAD3 genomes AF: 0.0275 AC: 3071 AN: 111509 Hom.: 97 Cov.: 23 AF XY: 0.0286 AC XY: 964 AN XY: 33689

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0215

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.00247

Gnomad MID AF: 0.00420

Gnomad NFE AF: 0.00337

Gnomad OTH AF: 0.0254

GnomAD4 exome AF: 0.0265 AC: 6191 AN: 233527 Hom.: 305 Cov.: 3 AF XY: 0.0282 AC XY: 1839 AN XY: 65299

Gnomad4 AFR exome AF: 0.0339

Gnomad4 AMR exome AF: 0.0655

Gnomad4 ASJ exome AF: 0.0149

Gnomad4 EAS exome AF: 0.160

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.00335

Gnomad4 NFE exome AF: 0.00335

Gnomad4 OTH exome AF: 0.0256

GnomAD4 genome AF: 0.0276 AC: 3078 AN: 111568 Hom.: 100 Cov.: 23 AF XY: 0.0286 AC XY: 965 AN XY: 33758

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.0662

Gnomad4 ASJ AF: 0.0215

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.00247

Gnomad4 NFE AF: 0.00337

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0122 Hom.: 645

Bravo AF: 0.0323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.43

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: rs3027440; hg19: chrX-43626481;