X-43688062-A-G

Position:

• chrX-43688062-A-G

Variant summary

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

The NM_000240.4(MAOA):​c.168+4455A>G 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 0.71 (20180 hom., 22926 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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]

MAOA (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAOA	NM_000240.4	c.168+4455A>G		intron_variant		ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.-232+4455A>G		intron_variant			NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.168+4455A>G		intron_variant		1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 78597 AN: 110862 Hom.: 20185 Cov.: 23 AF XY: 0.691 AC XY: 22888 AN XY: 33108

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.714

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.713

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: 0.709 AC: 78625 AN: 110915 Hom.: 20180 Cov.: 23 AF XY: 0.691 AC XY: 22926 AN XY: 33171

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.709

Alfa AF: 0.736 Hom.: 34073

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.76

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: rs5906957; hg19: chrX-43547310;