Variant X-43655100-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT-CACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGTACCGGCACCGGCACCAGTACCCGCACCAGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001270458.2(MAOA):c.-1673_-1644dupAGTACCCGCACCAGTACCGGCACCGGCACC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00786 in 61,976 control chromosomes in the GnomAD database, including 30 homozygotes. There are 2 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0079 ( 30 hom., 2 hem., cov: 25)

Exomes 𝑓: 0.00065 ( 1 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

MAOA
NM_001270458.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 30 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOA	NM_001270458.2 link	c.-1673_-1644dupAGTACCCGCACCAGTACCGGCACCGGCACC		5_prime_UTR_variant	1/16		NP_001257387.1	P21397-2Q49A63

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000542639 link	c.-1673_-1644dupAGTACCCGCACCAGTACCGGCACCGGCACC		5_prime_UTR_variant	1/16	2		ENSP00000440846.1		P21397-2

Frequencies

GnomAD3 genomes

AF:

0.00783

AC:

485

AN:

61935

Hom.:

Cov.:

AF XY:

0.000105

AC XY:

AN XY:

19077

show subpopulations

Gnomad AFR

AF:

0.00553

Gnomad AMI

AF:

0.00890

Gnomad AMR

AF:

0.00635

Gnomad ASJ

AF:

0.00693

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.00156

Gnomad FIN

AF:

0.00335

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0114

Gnomad OTH

AF:

0.00727

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000653

AC:

AN:

3062

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

1330

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000896

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00786

AC:

487

AN:

61976

Hom.:

Cov.:

AF XY:

0.000105

AC XY:

AN XY:

19116

show subpopulations

Gnomad4 AFR

AF:

0.00557

Gnomad4 AMR

AF:

0.00651

Gnomad4 ASJ

AF:

0.00693

Gnomad4 EAS

AF:

0.00175

Gnomad4 SAS

AF:

0.00157

Gnomad4 FIN

AF:

0.00335

Gnomad4 NFE

AF:

0.0114

Gnomad4 OTH

AF:

0.00713

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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