rs7879356

Variant names:

• chrX-43797137-T-C
• rs7879356
• NM_000898.5:c.606A>G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_000898.5(MAOB):​c.606A>G​(p.Thr202Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00819 in 1,206,381 control chromosomes in the GnomAD database, including 527 homozygotes. There are 2,661 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 0.043 (285 hom., 1273 hem., cov: 22)
  • Exomes 𝑓: 0.0046 (242 hom. 1388 hem.)
• Consequence: MAOB NM_000898.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP7: Synonymous conserved (PhyloP=1.12 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOB	NM_000898.5	c.606A>G	p.Thr202Thr	synonymous_variant	Exon 6 of 15	ENST00000378069.5	NP_000889.3
MAOB	XM_017029524.3	c.558A>G	p.Thr186Thr	synonymous_variant	Exon 6 of 15		XP_016885013.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOB	ENST00000378069.5	c.606A>G	p.Thr202Thr	synonymous_variant	Exon 6 of 15	1	NM_000898.5	ENSP00000367309.4
MAOB	ENST00000487544.1	n.*75A>G		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 4812 AN: 111552 Hom.: 287 Cov.: 22 AF XY: 0.0372 AC XY: 1258 AN XY: 33782

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000757

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00417

Gnomad NFE AF: 0.000357

Gnomad OTH AF: 0.0404

GnomAD3 exomes AF: 0.0123 AC: 2179 AN: 177814 Hom.: 120 AF XY: 0.00816 AC XY: 511 AN XY: 62624

Gnomad AFR exome AF: 0.153

Gnomad AMR exome AF: 0.00533

Gnomad ASJ exome AF: 0.000138

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000172

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000274

Gnomad OTH exome AF: 0.00550

GnomAD4 exome AF: 0.00462 AC: 5058 AN: 1094778 Hom.: 242 Cov.: 28 AF XY: 0.00385 AC XY: 1388 AN XY: 360424

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.00756

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000357

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000117

Gnomad4 OTH exome AF: 0.0114

GnomAD4 genome AF: 0.0433 AC: 4827 AN: 111603 Hom.: 285 Cov.: 22 AF XY: 0.0376 AC XY: 1273 AN XY: 33843

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000759

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000358

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.00772 Hom.: 374

Bravo AF: 0.0503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	2.8
DANN	Benign	0.53

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: rs7879356; hg19: chrX-43656384;