X-43810702-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000898.5(MAOB):​c.280-7298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 111,865 control chromosomes in the GnomAD database, including 423 homozygotes. There are 2,051 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 0.064 ( 423 hom., 2051 hem., cov: 23)

Consequence

MAOB
NM_000898.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.595

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAOBNM_000898.5 linkc.280-7298T>C intron_variant Intron 3 of 14 ENST00000378069.5 NP_000889.3 P27338-1
MAOBXM_017029524.3 linkc.232-7298T>C intron_variant Intron 3 of 14 XP_016885013.1 B7Z242

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAOBENST00000378069.5 linkc.280-7298T>C intron_variant Intron 3 of 14 1 NM_000898.5 ENSP00000367309.4 P27338-1
MAOBENST00000487544.1 linkn.606-7298T>C intron_variant Intron 4 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.0636
AC:
7109
AN:
111812
Hom.:
421
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.184
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0288
Gnomad ASJ
AF:
0.0166
Gnomad EAS
AF:
0.101
Gnomad SAS
AF:
0.176
Gnomad FIN
AF:
0.00164
Gnomad MID
AF:
0.00840
Gnomad NFE
AF:
0.00355
Gnomad OTH
AF:
0.0632
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0637
AC:
7127
AN:
111865
Hom.:
423
Cov.:
23
AF XY:
0.0602
AC XY:
2051
AN XY:
34055
show subpopulations
African (AFR)
AF:
0.184
AC:
5647
AN:
30643
American (AMR)
AF:
0.0287
AC:
304
AN:
10597
Ashkenazi Jewish (ASJ)
AF:
0.0166
AC:
44
AN:
2648
East Asian (EAS)
AF:
0.101
AC:
357
AN:
3538
South Asian (SAS)
AF:
0.174
AC:
463
AN:
2654
European-Finnish (FIN)
AF:
0.00164
AC:
10
AN:
6083
Middle Eastern (MID)
AF:
0.00922
AC:
2
AN:
217
European-Non Finnish (NFE)
AF:
0.00355
AC:
189
AN:
53260
Other (OTH)
AF:
0.0723
AC:
111
AN:
1536
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
213
426
640
853
1066
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
78
156
234
312
390
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0125
Hom.:
428
Bravo
AF:
0.0722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.58
DANN
Benign
0.37
PhyloP100
-0.59
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

Publications

Other links and lift over

dbSNP: rs12394221; hg19: chrX-43669949; API