X-43700329-G-A

Position:

• chrX-43700329-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):​c.306+6901G>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 0.66 (17514 hom., 21331 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.306+6901G>A		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.-94+6901G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.306+6901G>A		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 73255 AN: 110717 Hom.: 17511 Cov.: 23 AF XY: 0.646 AC XY: 21286 AN XY: 32939

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.644

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: 0.662 AC: 73297 AN: 110769 Hom.: 17514 Cov.: 23 AF XY: 0.646 AC XY: 21331 AN XY: 33001

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.642

Alfa AF: 0.671 Hom.: 33644

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.82
DANN	Benign	0.69

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: rs2283724; hg19: chrX-43559576;