rs7673213

Positions:

• chr4-139318541-A-G
• chr4-139318541-A-T

Variant summary

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

The NM_057175.5(NAA15):​c.55-15633A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,078 control chromosomes in the GnomAD database, including 4,132 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 0.22 (4132 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: NAA15 NM_057175.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

Genes affected

NAA15 (HGNC:30782): (N-alpha-acetyltransferase 15, NatA auxiliary 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 the auxillary subunit of the N-terminal acetyltransferase A (NatA) complex. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA15	NM_057175.5	c.55-15633A>G		intron_variant		ENST00000296543.10
NAA15	NM_001410842.1	c.55-15633A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA15	ENST00000296543.10	c.55-15633A>G		intron_variant		1	NM_057175.5	P3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33789 AN: 151954 Hom.: 4128 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.222 AC: 33803 AN: 152072 Hom.: 4132 Cov.: 32 AF XY: 0.222 AC XY: 16516 AN XY: 74352

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.221

Alfa AF: 0.195 Hom.: 627

Bravo AF: 0.219

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.65

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: rs7673213; hg19: chr4-140239695;