rs909525

chrX-43693955-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.306+527C>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 0.66 (17474 hom., 20961 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

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=-0.79).
• BS2: High Homozygotes in GnomAd at 17471 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.306+527C>T		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.-94+527C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.306+527C>T		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.660 AC: 72814 AN: 110291 Hom.: 17471 Cov.: 22 AF XY: 0.643 AC XY: 20914 AN XY: 32533

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.646

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: 0.660 AC: 72858 AN: 110346 Hom.: 17474 Cov.: 22 AF XY: 0.643 AC XY: 20961 AN XY: 32598

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.643

Alfa AF: 0.663 Hom.: 45919

Bravo AF: 0.672

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.1
Dann	Benign	0.48

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: rs909525; hg19: chrX-43553202;