rs2566970

chr3-113743276-C-T

Variant summary

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

The NM_025146.4(NAA50):c.8+2666G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,020 control chromosomes in the GnomAD database, including 9,819 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 0.36 (9819 hom., cov: 32)
• Consequence: NAA50 NM_025146.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

NAA50 (HGNC:29533): (N-alpha-acetyltransferase 50, NatE catalytic subunit) Enables H4 histone acetyltransferase activity; peptide alpha-N-acetyltransferase activity; and peptidyl-lysine acetyltransferase activity. Involved in N-terminal protein amino acid acetylation; establishment of mitotic sister chromatid cohesion; and mitotic sister chromatid cohesion, centromeric. Located in cytosol and nucleus. Part of NatA complex. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA50	NM_025146.4	c.8+2666G>A		intron_variant		ENST00000240922.8
NAA50	NM_001308445.2	c.8+2666G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA50	ENST00000240922.8	c.8+2666G>A		intron_variant		1	NM_025146.4	P4

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54357 AN: 151902 Hom.: 9807 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.358 AC: 54398 AN: 152020 Hom.: 9819 Cov.: 32 AF XY: 0.359 AC XY: 26705 AN XY: 74292

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.322

Alfa AF: 0.357 Hom.: 1980

Bravo AF: 0.347

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.69
Dann	Benign	0.57

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: rs2566970; hg19: chr3-113462123;