rs1465107

Variant names:

• chrX-43678769-A-G
• rs1465107
• NM_000240.4:c.74-4744A>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.74-4744A>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 0.69 (18952 hom., 21919 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 7 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: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, G2P

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	NM_000240.4	MANE Select	c.74-4744A>G		intron	N/A	NP_000231.1	Q53YE7
	MAOA	NM_001270458.2		c.-326-4744A>G		intron	N/A	NP_001257387.1	P21397-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	ENST00000338702.4	TSL:1 MANE Select	c.74-4744A>G		intron	N/A	ENSP00000340684.3	P21397-1
	MAOA	ENST00000967111.1		c.74-4744A>G		intron	N/A	ENSP00000637170.1
	MAOA	ENST00000873971.1		c.74-4744A>G		intron	N/A	ENSP00000544030.1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 75909 AN: 110668 Hom.: 18951 Cov.: 23

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.695

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.682

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: 0.686 AC: 75948 AN: 110717 Hom.: 18952 Cov.: 23 AF XY: 0.665 AC XY: 21919 AN XY: 32951

African (AFR) AF: 0.732 AC: 22284 AN: 30454

American (AMR) AF: 0.695 AC: 7207 AN: 10374

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 1818 AN: 2638

East Asian (EAS) AF: 0.422 AC: 1475 AN: 3499

South Asian (SAS) AF: 0.378 AC: 1013 AN: 2679

European-Finnish (FIN) AF: 0.556 AC: 3231 AN: 5807

Middle Eastern (MID) AF: 0.702 AC: 151 AN: 215

European-Non Finnish (NFE) AF: 0.706 AC: 37298 AN: 52866

Other (OTH) AF: 0.679 AC: 1027 AN: 1512

Alfa AF: 0.695 Hom.: 5536

Bravo AF: 0.699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		0.19
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: rs1465107; hg19: chrX-43538017;