rs3027405

Positions:

• chrX-43737082-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000240.4(MAOA):​c.1106+802A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 111,741 control chromosomes in the GnomAD database, including 734 homozygotes. There are 2,850 hemizygotes in GnomAD. 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 0.096 (734 hom., 2850 hem., cov: 22)
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.1106+802A>T		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.707+802A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.1106+802A>T		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 10713 AN: 111686 Hom.: 733 Cov.: 22 AF XY: 0.0836 AC XY: 2831 AN XY: 33872

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0733

Gnomad EAS AF: 0.000281

Gnomad SAS AF: 0.0212

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.0962

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.0961 AC: 10736 AN: 111741 Hom.: 734 Cov.: 22 AF XY: 0.0840 AC XY: 2850 AN XY: 33937

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0733

Gnomad4 EAS AF: 0.000282

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0813

Alfa AF: 0.0748 Hom.: 393

Bravo AF: 0.108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.62

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: rs3027405; hg19: chrX-43596329;