NM_000240.4:c.1053-46A>T

Variant names:

• chrX-43736181-A-T
• rs2235186
• NM_000240.4:c.1053-46A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000240.4(MAOA):​c.1053-46A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000109 in 914,315 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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: not found (cov: 23)
  • Exomes 𝑓: 0.0000011 (0 hom. 0 hem.)
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 0 publications found

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)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000240.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	NM_000240.4	MANE Select	c.1053-46A>T		intron	N/A	NP_000231.1
	MAOA	NM_001270458.2		c.654-46A>T		intron	N/A	NP_001257387.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	ENST00000338702.4	TSL:1 MANE Select	c.1053-46A>T		intron	N/A	ENSP00000340684.3
	MAOA	ENST00000693128.1		c.948-46A>T		intron	N/A	ENSP00000508493.1
	MAOA	ENST00000542639.6	TSL:2	c.654-46A>T		intron	N/A	ENSP00000440846.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 0.00000109 AC: 1 AN: 914315 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 259717

African (AFR) AF: 0.00 AC: 0 AN: 22904

American (AMR) AF: 0.00 AC: 0 AN: 33578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17558

East Asian (EAS) AF: 0.00 AC: 0 AN: 27873

South Asian (SAS) AF: 0.00 AC: 0 AN: 48968

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38135

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3704

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 682477

Other (OTH) AF: 0.0000256 AC: 1 AN: 39118

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.54
PhyloP100		0.036

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

Other links and lift over

dbSNP: rs2235186; hg19: chrX-43595428;