Variant X-43736496-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):c.1106+216A>G 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 ( 21058 hom., 22692 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

MAOA
NM_000240.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.334

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOA	NM_000240.4 link	c.1106+216A>G		intron_variant		ENST00000338702.4	NP_000231.1	P21397-1Q53YE7Q49A63
MAOA	NM_001270458.2 link	c.707+216A>G		intron_variant			NP_001257387.1	P21397-2Q49A63

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4 link	c.1106+216A>G		intron_variant		1	NM_000240.4	ENSP00000340684.3		P21397-1

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

79416

AN:

109949

Hom.:

21058

Cov.:

AF XY:

0.704

AC XY:

22646

AN XY:

32185

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

0.565

Gnomad AMR

AF:

0.711

Gnomad ASJ

AF:

0.711

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.742

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.716

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.722

AC:

79458

AN:

110004

Hom.:

21058

Cov.:

AF XY:

0.704

AC XY:

22692

AN XY:

32250

show subpopulations

Gnomad4 AFR

AF:

0.852

Gnomad4 AMR

AF:

0.710

Gnomad4 ASJ

AF:

0.711

Gnomad4 EAS

AF:

0.428

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.702

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.612

Hom.:

3696

Bravo

AF:

0.736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.4

DANN

Benign

0.50

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over