rs2239448

chrX-43743432-T-CchrX-43743432-T-G

Variant summary

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

The NM_000240.4(MAOA):c.1263-362T>C 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 0.65 (16899 hom., 19429 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

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=-0.93).
• BS2: High Homozygotes in GnomAd at 16902 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.1263-362T>C		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.864-362T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.1263-362T>C		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 70396 AN: 108498 Hom.: 16902 Cov.: 21 AF XY: 0.628 AC XY: 19390 AN XY: 30890

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.727

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.655

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: 0.649 AC: 70426 AN: 108555 Hom.: 16899 Cov.: 21 AF XY: 0.628 AC XY: 19429 AN XY: 30957

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.652

Alfa AF: 0.677 Hom.: 5325

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.99
Dann	Benign	0.44

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: rs2239448; hg19: chrX-43602679;