rs5905859

Variant names:

• chrX-43732253-C-A
• rs5905859
• NM_000240.4:c.955+400C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-43732253-C-A
• chrX-43732253-C-G
• chrX-43732253-C-T

Variant summary

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

The NM_000240.4(MAOA):​c.955+400C>A 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 0.54 (12441 hom., 17617 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 9 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=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000240.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	NM_000240.4	MANE Select	c.955+400C>A		intron	N/A	NP_000231.1
	MAOA	NM_001270458.2		c.556+400C>A		intron	N/A	NP_001257387.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAOA	ENST00000338702.4	TSL:1 MANE Select	c.955+400C>A		intron	N/A	ENSP00000340684.3
	MAOA	ENST00000693128.1		c.850+400C>A		intron	N/A	ENSP00000508493.1
	MAOA	ENST00000542639.6	TSL:2	c.556+400C>A		intron	N/A	ENSP00000440846.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 60140 AN: 110433 Hom.: 12452 Cov.: 23

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.556

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: 0.544 AC: 60138 AN: 110490 Hom.: 12441 Cov.: 23 AF XY: 0.537 AC XY: 17617 AN XY: 32778

African (AFR) AF: 0.329 AC: 10013 AN: 30401

American (AMR) AF: 0.626 AC: 6499 AN: 10390

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 1651 AN: 2636

East Asian (EAS) AF: 0.422 AC: 1452 AN: 3440

South Asian (SAS) AF: 0.355 AC: 935 AN: 2631

European-Finnish (FIN) AF: 0.597 AC: 3494 AN: 5850

Middle Eastern (MID) AF: 0.616 AC: 130 AN: 211

European-Non Finnish (NFE) AF: 0.659 AC: 34762 AN: 52757

Other (OTH) AF: 0.553 AC: 829 AN: 1499

Alfa AF: 0.579 Hom.: 12425

Bravo AF: 0.538

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.74
PhyloP100		-0.26
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: rs5905859; hg19: chrX-43591500;