rs3788863

Positions:

• chrX-43665517-T-A

Variant summary

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

The NM_000240.4(MAOA):​c.73+9103T>A 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 0.69 (19098 hom., 21657 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.73+9103T>A		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.-327+7548T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.73+9103T>A		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 75811 AN: 109939 Hom.: 19096 Cov.: 22 AF XY: 0.670 AC XY: 21606 AN XY: 32227

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.687

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: 0.690 AC: 75859 AN: 109998 Hom.: 19098 Cov.: 22 AF XY: 0.671 AC XY: 21657 AN XY: 32296

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.684

Alfa AF: 0.706 Hom.: 4320

Bravo AF: 0.702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.80

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

Other links and lift over

dbSNP: rs3788863; hg19: chrX-43524765;