rs5905702

Positions:

• chrX-43658940-T-G

Variant summary

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

The NM_000240.4(MAOA):​c.73+2526T>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 0.60 (15004 hom., 19072 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.73+2526T>G		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.-327+971T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.73+2526T>G		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 66411 AN: 109993 Hom.: 15011 Cov.: 22 AF XY: 0.590 AC XY: 19048 AN XY: 32265

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.615

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: 0.604 AC: 66418 AN: 110041 Hom.: 15004 Cov.: 22 AF XY: 0.590 AC XY: 19072 AN XY: 32323

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.612

Alfa AF: 0.688 Hom.: 35236

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.77

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: rs5905702; hg19: chrX-43518188; COSMIC: COSV58643147;