chr20-20025724-T-A

Variant names:

• chr20-20025724-T-A
• rs7263
• NM_016100.5:c.126T>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_016100.5(NAA20):​c.126T>A​(p.Tyr42*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NAA20 NM_016100.5 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 15 publications found

Genes affected

NAA20 (HGNC:15908): (N-alpha-acetyltransferase 20, NatB catalytic subunit) NAT5 is a component of N-acetyltransferase complex B (NatB). Human NatB performs cotranslational N(alpha)-terminal acetylation of methionine residues when they are followed by asparagine (Starheim et al., 2008 [PubMed 18570629]).[supplied by OMIM, Apr 2009]

NAA20 Gene-Disease associations (from GenCC):

• intellectual developmental disorder, autosomal recessive 73

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016100.5. 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
	NAA20	NM_016100.5	MANE Select	c.126T>A	p.Tyr42*	stop_gained	Exon 3 of 6	NP_057184.1
	NAA20	NM_181527.3		c.90T>A	p.Tyr30*	stop_gained	Exon 3 of 6	NP_852668.1
	NAA20	NM_181528.3		c.126T>A	p.Tyr42*	stop_gained	Exon 3 of 5	NP_852669.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA20	ENST00000334982.9	TSL:1 MANE Select	c.126T>A	p.Tyr42*	stop_gained	Exon 3 of 6	ENSP00000335636.4
	NAA20	ENST00000398602.2	TSL:5	c.90T>A	p.Tyr30*	stop_gained	Exon 3 of 6	ENSP00000381603.2
	NAA20	ENST00000310450.8	TSL:2	c.126T>A	p.Tyr42*	stop_gained	Exon 3 of 5	ENSP00000311027.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1941

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.53
CADD	Pathogenic	35
DANN	Uncertain	1.0
Eigen	Uncertain	0.27
Eigen_PC	Benign	-0.016
FATHMM_MKL	Uncertain	0.78	D
PhyloP100		-0.064
Vest4		0.55
GERP RS		-1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=8/192	disease causing (fs/PTC)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs7263; hg19: chr20-20006368;