rs12894584

Variant names:

• chr14-57396667-C-T
• rs12894584
• NM_001011713.3:c.772-85C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001011713.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA30	NM_001011713.3	MANE Select	c.772-85C>T		intron	N/A	NP_001011713.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA30	ENST00000556492.6	TSL:1 MANE Select	c.772-85C>T		intron	N/A	ENSP00000452521.1
	NAA30	ENST00000298406.6	TSL:1	c.205-85C>T		intron	N/A	ENSP00000298406.6
	NAA30	ENST00000554703.1	TSL:1	c.-3-85C>T		intron	N/A	ENSP00000451255.1

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

African (AFR) AF: 0.0429 AC: 1312 AN: 30558

American (AMR) AF: 0.129 AC: 5514 AN: 42896

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 5708 AN: 23694

East Asian (EAS) AF: 0.000414 AC: 16 AN: 38670

South Asian (SAS) AF: 0.122 AC: 8761 AN: 71908

European-Finnish (FIN) AF: 0.231 AC: 11556 AN: 50078

Middle Eastern (MID) AF: 0.212 AC: 1125 AN: 5298

European-Non Finnish (NFE) AF: 0.291 AC: 282570 AN: 970508

Other (OTH) AF: 0.233 AC: 12438 AN: 53282

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

African (AFR) AF: 0.0506 AC: 2100 AN: 41538

American (AMR) AF: 0.177 AC: 2709 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.123 AC: 594 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10572

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19713 AN: 67986

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.233 Hom.: 3588

Bravo AF: 0.181

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.9
DANN	Benign	0.67
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12894584; hg19: chr14-57863385;