rs5905702

Variant names:

• chrX-43658940-T-G
• rs5905702
• NM_000240.4:c.73+2526T>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.73+2526T>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 0.60 (15004 hom., 19072 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 3 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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4	c.73+2526T>G		intron_variant	Intron 1 of 14	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.-327+971T>G		intron_variant	Intron 2 of 15		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.73+2526T>G		intron_variant	Intron 1 of 14	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 66411 AN: 109993 Hom.: 15011 Cov.: 22

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.615

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: 0.604 AC: 66418 AN: 110041 Hom.: 15004 Cov.: 22 AF XY: 0.590 AC XY: 19072 AN XY: 32323

African (AFR) AF: 0.447 AC: 13493 AN: 30194

American (AMR) AF: 0.665 AC: 6843 AN: 10296

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 1783 AN: 2625

East Asian (EAS) AF: 0.422 AC: 1466 AN: 3470

South Asian (SAS) AF: 0.380 AC: 994 AN: 2619

European-Finnish (FIN) AF: 0.559 AC: 3211 AN: 5745

Middle Eastern (MID) AF: 0.687 AC: 149 AN: 217

European-Non Finnish (NFE) AF: 0.704 AC: 37106 AN: 52692

Other (OTH) AF: 0.612 AC: 925 AN: 1511

Alfa AF: 0.677 Hom.: 46542

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.77
PhyloP100		-0.011
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: rs5905702; hg19: chrX-43518188; COSMIC: COSV58643147;