rs2283725

Variant names:

• chrX-43700729-A-G
• rs2283725
• NM_000240.4:c.306+7301A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-43700729-A-G
• chrX-43700729-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):​c.306+7301A>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 0.65 (16928 hom., 21012 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• Publications: 14 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4	c.306+7301A>G		intron_variant	Intron 3 of 14	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.-94+7301A>G		intron_variant	Intron 4 of 15		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.306+7301A>G		intron_variant	Intron 3 of 14	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.650 AC: 72119 AN: 110904 Hom.: 16928 Cov.: 23

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.636

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: 0.650 AC: 72152 AN: 110957 Hom.: 16928 Cov.: 23 AF XY: 0.633 AC XY: 21012 AN XY: 33171

African (AFR) AF: 0.688 AC: 21013 AN: 30526

American (AMR) AF: 0.664 AC: 6916 AN: 10419

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 1637 AN: 2635

East Asian (EAS) AF: 0.422 AC: 1485 AN: 3520

South Asian (SAS) AF: 0.365 AC: 970 AN: 2659

European-Finnish (FIN) AF: 0.545 AC: 3189 AN: 5856

Middle Eastern (MID) AF: 0.600 AC: 126 AN: 210

European-Non Finnish (NFE) AF: 0.669 AC: 35404 AN: 52936

Other (OTH) AF: 0.633 AC: 964 AN: 1522

Alfa AF: 0.668 Hom.: 39824

Bravo AF: 0.661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.76
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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: rs2283725; hg19: chrX-43559976;