rs12894584

Positions:

• chr14-57396667-C-T

Variant summary

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

The NM_001011713.3(NAA30):​c.772-85C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 1,439,060 control chromosomes in the GnomAD database, including 50,057 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 0.19 (3728 hom., cov: 33)
  • Exomes 𝑓: 0.26 (46329 hom.)
• Consequence: NAA30 NM_001011713.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

NAA30 (HGNC:19844): (N-alpha-acetyltransferase 30, NatC catalytic subunit) Enables peptide alpha-N-acetyltransferase activity. Involved in N-terminal peptidyl-methionine acetylation. Located in cytosol and nucleus. Part of NatC complex. Colocalizes with polysome. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAA30	NM_001011713.3	c.772-85C>T		intron_variant		ENST00000556492.6	NP_001011713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA30	ENST00000556492.6	c.772-85C>T		intron_variant		1	NM_001011713.3	ENSP00000452521	P1
NAA30	ENST00000298406.6	c.207-85C>T		intron_variant		1		ENSP00000298406
NAA30	ENST00000554703.1	c.-3-85C>T		intron_variant		1		ENSP00000451255
NAA30	ENST00000555166.5	c.-3-85C>T		intron_variant		2		ENSP00000450939

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29133 AN: 152050 Hom.: 3729 Cov.: 33

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.256 AC: 329000 AN: 1286892 Hom.: 46329 AF XY: 0.254 AC XY: 163090 AN XY: 641784

Gnomad4 AFR exome AF: 0.0429

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.241

Gnomad4 EAS exome AF: 0.000414

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.231

Gnomad4 NFE exome AF: 0.291

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.191 AC: 29124 AN: 152168 Hom.: 3728 Cov.: 33 AF XY: 0.185 AC XY: 13796 AN XY: 74382

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.221

Alfa AF: 0.255 Hom.: 3224

Bravo AF: 0.181

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.9
DANN	Benign	0.67

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: rs12894584; hg19: chr14-57863385;