chrX-43742116-A-G

Position:

• chrX-43742116-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.1262+69A>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 0.65 (16945 hom., 21101 hem., cov: 23)
  • Exomes 𝑓: 0.68 (171826 hom. 236366 hem.)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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	Protein	UniProt
MAOA	NM_000240.4	c.1262+69A>G		intron_variant		ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.863+69A>G		intron_variant			NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.1262+69A>G		intron_variant		1	NM_000240.4	ENSP00000340684	P1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 72236 AN: 110936 Hom.: 16951 Cov.: 23 AF XY: 0.635 AC XY: 21065 AN XY: 33152

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.730

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.659

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.678 AC: 734750 AN: 1084239 Hom.: 171826 AF XY: 0.670 AC XY: 236366 AN XY: 353027

Gnomad4 AFR exome AF: 0.605

Gnomad4 AMR exome AF: 0.675

Gnomad4 ASJ exome AF: 0.715

Gnomad4 EAS exome AF: 0.430

Gnomad4 SAS exome AF: 0.414

Gnomad4 FIN exome AF: 0.624

Gnomad4 NFE exome AF: 0.708

Gnomad4 OTH exome AF: 0.663

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.651 AC: 72259 AN: 110989 Hom.: 16945 Cov.: 23 AF XY: 0.635 AC XY: 21101 AN XY: 33215

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.655

Alfa AF: 0.696 Hom.: 36536

Bravo AF: 0.655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.035
DANN	Benign	0.62

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: rs979605; hg19: chrX-43601363; COSMIC: COSV58645473; COSMIC: COSV58645473;