20-20027937-T-C

Position:

• chr20-20027937-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016100.5(NAA20):​c.305+1018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,000 control chromosomes in the GnomAD database, including 10,324 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 0.34 (10324 hom., cov: 31)
• Consequence: NAA20 NM_016100.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA20	NM_016100.5	c.305+1018T>C		intron_variant		ENST00000334982.9
NAA20	NM_181527.3	c.269+1018T>C		intron_variant
NAA20	NM_181528.3	c.305+1018T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA20	ENST00000334982.9	c.305+1018T>C		intron_variant		1	NM_016100.5	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51129 AN: 151878 Hom.: 10324 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.342

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.336 AC: 51119 AN: 152000 Hom.: 10324 Cov.: 31 AF XY: 0.335 AC XY: 24874 AN XY: 74272

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.338

Alfa AF: 0.411 Hom.: 6637

Bravo AF: 0.314

Asia WGS AF: 0.236 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.85

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: rs6081840; hg19: chr20-20008581;