dbSNP rs979606: MAOA:c.1165-55C>T (chrX-43741895-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):c.1165-55C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.72 ( 21061 hom., 23394 hem., cov: 23)

Exomes 𝑓: 0.68 ( 176704 hom. 240565 hem. )

Failed GnomAD Quality Control

Consequence

MAOA
NM_000240.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.372

Publications

27 publications found

Variant links:

Genes affected

MAOA (HGNC:6833): (monoamine oxidase A) This gene is one of two neighboring gene family members that encode mitochondrial enzymes which catalyze the oxidative deamination of amines, such as dopamine, norepinephrine, and serotonin. Mutation of this gene results in Brunner syndrome. This gene has also been associated with a variety of other psychiatric disorders, including antisocial behavior. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Jul 2012]

MAOA Gene-Disease associations (from GenCC):

Brunner syndrome
Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

MAOA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4 link	c.1165-55C>T		intron_variant	Intron 11 of 14	ENST00000338702.4	NP_000231.1	P21397-1Q53YE7Q49A63
MAOA	NM_001270458.2 link	c.766-55C>T		intron_variant	Intron 12 of 15		NP_001257387.1	P21397-2Q49A63

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4 link	c.1165-55C>T		intron_variant	Intron 11 of 14	1	NM_000240.4	ENSP00000340684.3		P21397-1

Frequencies

GnomAD3 genomes

AF:

0.723

AC:

80129

AN:

110810

Hom.:

21061

Cov.:

show subpopulations

Gnomad AFR

AF:

0.853

Gnomad AMI

AF:

0.567

Gnomad AMR

AF:

0.711

Gnomad ASJ

AF:

0.712

Gnomad EAS

AF:

0.431

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.738

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.717

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.684

AC:

746321

AN:

1090492

Hom.:

176704

AF XY:

0.673

AC XY:

240565

AN XY:

357528

show subpopulations

African (AFR)

AF:

0.860

AC:

22639

AN:

26332

American (AMR)

AF:

0.687

AC:

23504

AN:

34197

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

13867

AN:

19197

East Asian (EAS)

AF:

0.429

AC:

12858

AN:

29972

South Asian (SAS)

AF:

0.413

AC:

21800

AN:

52826

European-Finnish (FIN)

AF:

0.620

AC:

24825

AN:

40009

Middle Eastern (MID)

AF:

0.728

AC:

2965

AN:

4071

European-Non Finnish (NFE)

AF:

0.707

AC:

592713

AN:

838042

Other (OTH)

AF:

0.679

AC:

31150

AN:

45846

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

7795

15590

23386

31181

38976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17530

35060

52590

70120

87650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.723

AC:

80172

AN:

110867

Hom.:

21061

Cov.:

AF XY:

0.707

AC XY:

23394

AN XY:

33083

show subpopulations

African (AFR)

AF:

0.853

AC:

26024

AN:

30503

American (AMR)

AF:

0.710

AC:

7383

AN:

10397

Ashkenazi Jewish (ASJ)

AF:

0.712

AC:

1871

AN:

2628

East Asian (EAS)

AF:

0.430

AC:

1507

AN:

3501

South Asian (SAS)

AF:

0.382

AC:

1009

AN:

2642

European-Finnish (FIN)

AF:

0.614

AC:

3608

AN:

5874

Middle Eastern (MID)

AF:

0.747

AC:

162

AN:

217

European-Non Finnish (NFE)

AF:

0.702

AC:

37155

AN:

52928

Other (OTH)

AF:

0.712

AC:

1072

AN:

1505

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

778

1556

2333

3111

3889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.721

Hom.:

51823

Bravo

AF:

0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.0

(source)

DANN

Benign

0.66

PhyloP100

0.37

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over