rs979606

Variant names:

• chrX-43741895-C-T
• rs979606
• NM_000240.4:c.1165-55C>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.1165-55C>T 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 0.72 (21061 hom., 23394 hem., cov: 23)
  • Exomes 𝑓: 0.68 (176704 hom. 240565 hem.)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4	c.1165-55C>T		intron_variant	Intron 11 of 14	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.766-55C>T		intron_variant	Intron 12 of 15		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.1165-55C>T		intron_variant	Intron 11 of 14	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.723 AC: 80129 AN: 110810 Hom.: 21061 Cov.: 23

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.738

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.717

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.684 AC: 746321 AN: 1090492 Hom.: 176704 AF XY: 0.673 AC XY: 240565 AN XY: 357528

Gnomad4 AFR exome AF: 0.860 AC: 22639 AN: 26332

Gnomad4 AMR exome AF: 0.687 AC: 23504 AN: 34197

Gnomad4 ASJ exome AF: 0.722 AC: 13867 AN: 19197

Gnomad4 EAS exome AF: 0.429 AC: 12858 AN: 29972

Gnomad4 SAS exome AF: 0.413 AC: 21800 AN: 52826

Gnomad4 FIN exome AF: 0.620 AC: 24825 AN: 40009

Gnomad4 NFE exome AF: 0.707 AC: 592713 AN: 838042

Gnomad4 Remaining exome AF: 0.679 AC: 31150 AN: 45846

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.723 AC: 80172 AN: 110867 Hom.: 21061 Cov.: 23 AF XY: 0.707 AC XY: 23394 AN XY: 33083

Gnomad4 AFR AF: 0.853 AC: 0.853162 AN: 0.853162

Gnomad4 AMR AF: 0.710 AC: 0.710109 AN: 0.710109

Gnomad4 ASJ AF: 0.712 AC: 0.711948 AN: 0.711948

Gnomad4 EAS AF: 0.430 AC: 0.430448 AN: 0.430448

Gnomad4 SAS AF: 0.382 AC: 0.381908 AN: 0.381908

Gnomad4 FIN AF: 0.614 AC: 0.614232 AN: 0.614232

Gnomad4 NFE AF: 0.702 AC: 0.701991 AN: 0.701991

Gnomad4 OTH AF: 0.712 AC: 0.712292 AN: 0.712292

Alfa AF: 0.721 Hom.: 51823

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.66
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

Publications

LitVar

Other links and lift over

dbSNP: rs979606; hg19: chrX-43601142; COSMIC: COSV58641955; COSMIC: COSV58641955;