rs979606

chrX-43741895-C-T

Variant summary

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

The NM_000240.4(MAOA):c.1165-55C>T 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 0.72 (21061 hom., 23394 hem., cov: 23)
  • Exomes 𝑓: 0.68 (176704 hom. 240565 hem.)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

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=-0.84).
• BS2: High Homozygotes in GnomAd at 21061 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.1165-55C>T		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.766-55C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.1165-55C>T		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 80129 AN: 110810 Hom.: 21061 Cov.: 23 AF XY: 0.707 AC XY: 23347 AN XY: 33016

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.738

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.717

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.684 AC: 746321 AN: 1090492 Hom.: 176704 AF XY: 0.673 AC XY: 240565 AN XY: 357528

Gnomad4 AFR exome AF: 0.860

Gnomad4 AMR exome AF: 0.687

Gnomad4 ASJ exome AF: 0.722

Gnomad4 EAS exome AF: 0.429

Gnomad4 SAS exome AF: 0.413

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.707

Gnomad4 OTH exome AF: 0.679

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.723 AC: 80172 AN: 110867 Hom.: 21061 Cov.: 23 AF XY: 0.707 AC XY: 23394 AN XY: 33083

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.712

Alfa AF: 0.716 Hom.: 39215

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.0
Dann	Benign	0.66

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: rs979606; hg19: chrX-43601142; COSMIC: COSV58641955; COSMIC: COSV58641955;