rs1557501

Positions:

• chrX-153931677-C-T

Variant summary

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

The NM_003491.4(NAA10):​c.386+394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 885,635 control chromosomes in the GnomAD database, including 26,364 homozygotes. There are 65,388 hemizygotes in GnomAD. 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 0.39 (8296 hom., 13255 hem., cov: 24)
  • Exomes 𝑓: 0.22 (18068 hom. 52133 hem.)
• Consequence: NAA10 NM_003491.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

Genes affected

NAA10 (HGNC:18704): (N-alpha-acetyltransferase 10, NatA catalytic subunit) N-alpha-acetylation is among the most common post-translational protein modifications in eukaryotic cells. This process involves the transfer of an acetyl group from acetyl-coenzyme A to the alpha-amino group on a nascent polypeptide and is essential for normal cell function. This gene encodes an N-terminal acetyltransferase that functions as the catalytic subunit of the major amino-terminal acetyltransferase A complex. Mutations in this gene are the cause of Ogden syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

NAA10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAA10	NM_003491.4	c.386+394G>A		intron_variant		ENST00000464845.6	NP_003482.1
NAA10	NM_001256120.2	c.368+394G>A		intron_variant			NP_001243049.1
NAA10	NM_001256119.2	c.341+639G>A		intron_variant			NP_001243048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA10	ENST00000464845.6	c.386+394G>A		intron_variant		1	NM_003491.4	ENSP00000417763.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 43885 AN: 111711 Hom.: 8290 Cov.: 24 AF XY: 0.390 AC XY: 13207 AN XY: 33907

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.0364

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.224 AC: 173051 AN: 773871 Hom.: 18068 Cov.: 30 AF XY: 0.228 AC XY: 52133 AN XY: 228605

Gnomad4 AFR exome AF: 0.718

Gnomad4 AMR exome AF: 0.568

Gnomad4 ASJ exome AF: 0.293

Gnomad4 EAS exome AF: 0.716

Gnomad4 SAS exome AF: 0.561

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.297

GnomAD4 genome AF: 0.393 AC: 43942 AN: 111764 Hom.: 8296 Cov.: 24 AF XY: 0.390 AC XY: 13255 AN XY: 33970

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.433

Alfa AF: 0.281 Hom.: 6406

Bravo AF: 0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1557501; hg19: chrX-153197130;