20-20025724-T-C

Position:

• chr20-20025724-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_016100.5(NAA20):​c.126T>C​(p.Tyr42Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 1,610,282 control chromosomes in the GnomAD database, including 4,599 homozygotes. 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 0.071 (432 hom., cov: 32)
  • Exomes 𝑓: 0.071 (4167 hom.)
• Consequence: NAA20 NM_016100.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP7: Synonymous conserved (PhyloP=-0.064 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAA20	NM_016100.5	c.126T>C	p.Tyr42Tyr	synonymous_variant	3/6	ENST00000334982.9	NP_057184.1
NAA20	NM_181527.3	c.90T>C	p.Tyr30Tyr	synonymous_variant	3/6		NP_852668.1
NAA20	NM_181528.3	c.126T>C	p.Tyr42Tyr	synonymous_variant	3/5		NP_852669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA20	ENST00000334982.9	c.126T>C	p.Tyr42Tyr	synonymous_variant	3/6	1	NM_016100.5	ENSP00000335636.4

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 10754 AN: 152154 Hom.: 425 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0780

GnomAD3 exomes AF: 0.0785 AC: 19738 AN: 251418 Hom.: 906 AF XY: 0.0768 AC XY: 10438 AN XY: 135888

Gnomad AFR exome AF: 0.0666

Gnomad AMR exome AF: 0.120

Gnomad ASJ exome AF: 0.0832

Gnomad EAS exome AF: 0.109

Gnomad SAS exome AF: 0.0825

Gnomad FIN exome AF: 0.0260

Gnomad NFE exome AF: 0.0711

Gnomad OTH exome AF: 0.0771

GnomAD4 exome AF: 0.0713 AC: 104022 AN: 1458010 Hom.: 4167 Cov.: 30 AF XY: 0.0713 AC XY: 51729 AN XY: 725548

Gnomad4 AFR exome AF: 0.0709

Gnomad4 AMR exome AF: 0.118

Gnomad4 ASJ exome AF: 0.0800

Gnomad4 EAS exome AF: 0.147

Gnomad4 SAS exome AF: 0.0792

Gnomad4 FIN exome AF: 0.0300

Gnomad4 NFE exome AF: 0.0682

Gnomad4 OTH exome AF: 0.0702

GnomAD4 genome AF: 0.0708 AC: 10779 AN: 152272 Hom.: 432 Cov.: 32 AF XY: 0.0692 AC XY: 5151 AN XY: 74470

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0849

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.0772

Alfa AF: 0.0706 Hom.: 1028

Bravo AF: 0.0767

Asia WGS AF: 0.107 AC: 371 AN: 3478

EpiCase AF: 0.0707

EpiControl AF: 0.0687

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.9
DANN	Benign	0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs7263; hg19: chr20-20006368; COSMIC: COSV58549442; COSMIC: COSV58549442;