rs7879356

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000898.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	NM_000898.5	MANE Select	c.606A>G	p.Thr202Thr	synonymous	Exon 6 of 15	NP_000889.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOB	ENST00000378069.5	TSL:1 MANE Select	c.606A>G	p.Thr202Thr	synonymous	Exon 6 of 15	ENSP00000367309.4
	MAOB	ENST00000487544.1	TSL:5	n.*75A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 4812 AN: 111552 Hom.: 287 Cov.: 22

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

GnomAD2 exomes AF: 0.0123 AC: 2179 AN: 177814 AF XY: 0.00816

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 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

African (AFR) AF: 0.157 AC: 4133 AN: 26310

American (AMR) AF: 0.00756 AC: 263 AN: 34801

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19298

East Asian (EAS) AF: 0.00 AC: 0 AN: 30129

South Asian (SAS) AF: 0.000357 AC: 19 AN: 53147

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40502

Middle Eastern (MID) AF: 0.00461 AC: 19 AN: 4123

European-Non Finnish (NFE) AF: 0.000117 AC: 98 AN: 840497

Other (OTH) AF: 0.0114 AC: 526 AN: 45971

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

African (AFR) AF: 0.148 AC: 4532 AN: 30559

American (AMR) AF: 0.0201 AC: 212 AN: 10549

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2640

East Asian (EAS) AF: 0.00 AC: 0 AN: 3530

South Asian (SAS) AF: 0.000759 AC: 2 AN: 2634

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6114

Middle Eastern (MID) AF: 0.00459 AC: 1 AN: 218

European-Non Finnish (NFE) AF: 0.000358 AC: 19 AN: 53142

Other (OTH) AF: 0.0398 AC: 61 AN: 1531

Alfa AF: 0.0176 Hom.: 1358

Bravo AF: 0.0503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		1.1
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: rs7879356; hg19: chrX-43656384;