chrX-43880740-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_000898.5(MAOB):​c.46+1514G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00763 in 111,847 control chromosomes in the GnomAD database, including 6 homozygotes. There are 256 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 0.0076 ( 6 hom., 256 hem., cov: 24)

Consequence

MAOB
NM_000898.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.538

Publications

1 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]

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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=-0.89).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00763 (853/111847) while in subpopulation AFR AF = 0.026 (799/30744). AF 95% confidence interval is 0.0245. There are 6 homozygotes in GnomAd4. There are 256 alleles in the male GnomAd4 subpopulation. Median coverage is 24. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAOBNM_000898.5 linkc.46+1514G>A intron_variant Intron 1 of 14 ENST00000378069.5 NP_000889.3 P27338-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAOBENST00000378069.5 linkc.46+1514G>A intron_variant Intron 1 of 14 1 NM_000898.5 ENSP00000367309.4 P27338-1
MAOBENST00000468431.1 linkn.50+1514G>A intron_variant Intron 1 of 2 3
MAOBENST00000487544.1 linkn.182+1514G>A intron_variant Intron 1 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.00761
AC:
851
AN:
111793
Hom.:
7
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.0260
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00378
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000752
Gnomad OTH
AF:
0.00666
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00763
AC:
853
AN:
111847
Hom.:
6
Cov.:
24
AF XY:
0.00751
AC XY:
256
AN XY:
34075
show subpopulations
African (AFR)
AF:
0.0260
AC:
799
AN:
30744
American (AMR)
AF:
0.00377
AC:
40
AN:
10607
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2647
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3548
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2658
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6046
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
217
European-Non Finnish (NFE)
AF:
0.0000752
AC:
4
AN:
53176
Other (OTH)
AF:
0.00657
AC:
10
AN:
1521
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
31
61
92
122
153
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<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:
0.00281
Hom.:
97
Bravo
AF:
0.00855

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.33
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

Publications

Other links and lift over

dbSNP: rs12391346; hg19: chrX-43739986; API