rs3027407

chrX-43745594-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.*1081A>G variant causes a 3 prime UTR 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 (16952 hom., 20416 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805

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=-0.81).
• BS2: High Homozygotes in GnomAd at 16955 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.*1081A>G		3_prime_UTR_variant	15/15	ENST00000338702.4
MAOA	NM_001270458.2	c.*1081A>G		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.*1081A>G		3_prime_UTR_variant	15/15	1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 71502 AN: 109890 Hom.: 16955 Cov.: 22 AF XY: 0.633 AC XY: 20377 AN XY: 32172

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.657

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.651 AC: 71532 AN: 109943 Hom.: 16952 Cov.: 22 AF XY: 0.633 AC XY: 20416 AN XY: 32235

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.654

Alfa AF: 0.677 Hom.: 5352

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.6
Dann	Benign	0.84

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: rs3027407; hg19: chrX-43604841;