rs3027400

Variant names:

• chrX-43733516-T-G
• rs3027400
• NM_000240.4:c.1052+721T>G

Variant summary

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

The NM_000240.4(MAOA):​c.1052+721T>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 0.72 (21082 hom., 23007 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 13 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.1052+721T>G		intron_variant	Intron 9 of 14	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.653+721T>G		intron_variant	Intron 10 of 15		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.1052+721T>G		intron_variant	Intron 9 of 14	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.722 AC: 79772 AN: 110444 Hom.: 21082 Cov.: 23

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.733

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.715

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: 0.722 AC: 79813 AN: 110496 Hom.: 21082 Cov.: 23 AF XY: 0.703 AC XY: 23007 AN XY: 32704

African (AFR) AF: 0.853 AC: 25896 AN: 30366

American (AMR) AF: 0.711 AC: 7390 AN: 10401

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 1868 AN: 2628

East Asian (EAS) AF: 0.425 AC: 1482 AN: 3484

South Asian (SAS) AF: 0.375 AC: 963 AN: 2570

European-Finnish (FIN) AF: 0.610 AC: 3584 AN: 5877

Middle Eastern (MID) AF: 0.743 AC: 159 AN: 214

European-Non Finnish (NFE) AF: 0.701 AC: 37016 AN: 52767

Other (OTH) AF: 0.711 AC: 1075 AN: 1512

Alfa AF: 0.718 Hom.: 47964

Bravo AF: 0.736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.7
DANN	Benign	0.76
PhyloP100		0.11
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: rs3027400; hg19: chrX-43592763;