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X-43843727-C-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_000898.5(MAOB):c.84G>T(p.Leu28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000734 in 1,209,094 control chromosomes in the GnomAD database, including 6 homozygotes. There are 218 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L28L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0037 ( 3 hom., 88 hem., cov: 23)
Exomes 𝑓: 0.00044 ( 3 hom. 130 hem. )

Consequence

MAOB
NM_000898.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.267
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 made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-43843727-C-A is Benign according to our data. Variant chrX-43843727-C-A is described in ClinVar as [Benign]. Clinvar id is 711252.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.267 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAOBNM_000898.5 linkuse as main transcriptc.84G>T p.Leu28= synonymous_variant 2/15 ENST00000378069.5
MAOBXM_017029524.3 linkuse as main transcriptc.36G>T p.Leu12= synonymous_variant 2/15

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAOBENST00000378069.5 linkuse as main transcriptc.84G>T p.Leu28= synonymous_variant 2/151 NM_000898.5 P1P27338-1
MAOBENST00000487544.1 linkuse as main transcriptn.410G>T non_coding_transcript_exon_variant 3/75

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00367
AC:
409
AN:
111354
Hom.:
3
Cov.:
23
AF XY:
0.00263
AC XY:
88
AN XY:
33510
show subpopulations
Gnomad AFR
AF:
0.0126
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00134
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:
0.0000753
Gnomad OTH
AF:
0.00401
GnomAD3 exomes
AF:
0.000992
AC:
181
AN:
182438
Hom.:
5
AF XY:
0.000552
AC XY:
37
AN XY:
66972
show subpopulations
Gnomad AFR exome
AF:
0.0123
Gnomad AMR exome
AF:
0.000479
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000491
Gnomad OTH exome
AF:
0.000669
GnomAD4 exome
AF:
0.000436
AC:
479
AN:
1097687
Hom.:
3
Cov.:
29
AF XY:
0.000358
AC XY:
130
AN XY:
363065
show subpopulations
Gnomad4 AFR exome
AF:
0.0143
Gnomad4 AMR exome
AF:
0.000455
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000392
Gnomad4 OTH exome
AF:
0.000912
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00367
AC:
409
AN:
111407
Hom.:
3
Cov.:
23
AF XY:
0.00262
AC XY:
88
AN XY:
33573
show subpopulations
Gnomad4 AFR
AF:
0.0126
Gnomad4 AMR
AF:
0.00134
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000753
Gnomad4 OTH
AF:
0.00396
Alfa
AF:
0.000652
Hom.:
15
Bravo
AF:
0.00400
EpiCase
AF:
0.0000547
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
Cadd
Benign
9.6
Dann
Benign
0.83

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12010260; hg19: chrX-43702973; API