rs1800659

Variant names:

• chrX-43714922-G-A
• rs1800659
• NM_000240.4:c.503+2126G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-43714922-G-A
• chrX-43714922-G-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.503+2126G>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 0.56 (13267 hom., 16424 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 4 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=-1.01).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	NM_000240.4	MANE Select	c.503+2126G>A		intron	N/A	NP_000231.1
	MAOA	NM_001270458.2		c.104+2126G>A		intron	N/A	NP_001257387.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	ENST00000338702.4	TSL:1 MANE Select	c.503+2126G>A		intron	N/A	ENSP00000340684.3
	MAOA	ENST00000693128.1		c.398+2126G>A		intron	N/A	ENSP00000508493.1
	MAOA	ENST00000542639.6	TSL:2	c.104+2126G>A		intron	N/A	ENSP00000440846.1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 60012 AN: 107689 Hom.: 13276 Cov.: 20

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.667

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.585

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: 0.557 AC: 60011 AN: 107737 Hom.: 13267 Cov.: 20 AF XY: 0.543 AC XY: 16424 AN XY: 30241

African (AFR) AF: 0.315 AC: 9343 AN: 29627

American (AMR) AF: 0.639 AC: 6416 AN: 10045

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 1777 AN: 2594

East Asian (EAS) AF: 0.416 AC: 1387 AN: 3337

South Asian (SAS) AF: 0.366 AC: 890 AN: 2433

European-Finnish (FIN) AF: 0.592 AC: 3270 AN: 5523

Middle Eastern (MID) AF: 0.675 AC: 137 AN: 203

European-Non Finnish (NFE) AF: 0.686 AC: 35582 AN: 51864

Other (OTH) AF: 0.582 AC: 844 AN: 1450

Alfa AF: 0.637 Hom.: 49471

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.23
PhyloP100		-0.24
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: rs1800659; hg19: chrX-43574169;