rs2283724

Variant names:

• chrX-43700329-G-A
• rs2283724
• NM_000240.4:c.306+6901G>A

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+6901G>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 0.66 (17514 hom., 21331 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 8 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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4	c.306+6901G>A		intron_variant	Intron 3 of 14	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.-94+6901G>A		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+6901G>A		intron_variant	Intron 3 of 14	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 73255 AN: 110717 Hom.: 17511 Cov.: 23

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.644

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: 0.662 AC: 73297 AN: 110769 Hom.: 17514 Cov.: 23 AF XY: 0.646 AC XY: 21331 AN XY: 33001

African (AFR) AF: 0.724 AC: 22083 AN: 30484

American (AMR) AF: 0.671 AC: 6989 AN: 10423

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 1634 AN: 2636

East Asian (EAS) AF: 0.422 AC: 1469 AN: 3481

South Asian (SAS) AF: 0.363 AC: 960 AN: 2647

European-Finnish (FIN) AF: 0.550 AC: 3208 AN: 5830

Middle Eastern (MID) AF: 0.610 AC: 130 AN: 213

European-Non Finnish (NFE) AF: 0.670 AC: 35417 AN: 52884

Other (OTH) AF: 0.642 AC: 963 AN: 1501

Alfa AF: 0.675 Hom.: 52645

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.82
DANN	Benign	0.69
PhyloP100		-0.16
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: rs2283724; hg19: chrX-43559576;