rs3027407

Variant names:

• chrX-43745594-A-G
• rs3027407
• NM_000240.4:c.*1081A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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
• Publications: 20 publications found

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 Gene-Disease associations (from GenCC):

• Brunner syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4	c.*1081A>G		3_prime_UTR_variant	Exon 15 of 15	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.*1081A>G		3_prime_UTR_variant	Exon 16 of 16		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.*1081A>G		3_prime_UTR_variant	Exon 15 of 15	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.651 AC: 71502 AN: 109890 Hom.: 16955 Cov.: 22

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 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

African (AFR) AF: 0.624 AC: 18816 AN: 30164

American (AMR) AF: 0.630 AC: 6494 AN: 10316

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 1898 AN: 2626

East Asian (EAS) AF: 0.420 AC: 1457 AN: 3471

South Asian (SAS) AF: 0.369 AC: 944 AN: 2560

European-Finnish (FIN) AF: 0.611 AC: 3517 AN: 5755

Middle Eastern (MID) AF: 0.731 AC: 158 AN: 216

European-Non Finnish (NFE) AF: 0.701 AC: 36899 AN: 52672

Other (OTH) AF: 0.654 AC: 976 AN: 1493

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
PhyloP100		0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3027407; hg19: chrX-43604841;