rs1800659

chrX-43714922-G-AchrX-43714922-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAd at 13276 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.503+2126G>A		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.104+2126G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.503+2126G>A		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 60012 AN: 107689 Hom.: 13276 Cov.: 20 AF XY: 0.544 AC XY: 16410 AN XY: 30183

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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.582

Alfa AF: 0.663 Hom.: 33487

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.23

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800659; hg19: chrX-43574169;