rs12843268

chrX-43714419-A-G

Variant summary

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

The NM_000240.4(MAOA):c.503+1623A>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 0.57 (13637 hom., 17389 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-1.0).
• BS2: High Homozygotes in GnomAd at 13648 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.503+1623A>G		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.104+1623A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.503+1623A>G		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 61649 AN: 108942 Hom.: 13648 Cov.: 21 AF XY: 0.555 AC XY: 17373 AN XY: 31282

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.591

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: 0.566 AC: 61649 AN: 108994 Hom.: 13637 Cov.: 21 AF XY: 0.555 AC XY: 17389 AN XY: 31344

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.588

Alfa AF: 0.675 Hom.: 36344

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.35

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: rs12843268; hg19: chrX-43573666;