4-139334493-GA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_057175.5(NAA15):c.139+238del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,112 control chromosomes in the GnomAD database, including 5,677 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (5677 hom., cov: 22)
• Consequence: NAA15 NM_057175.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.361

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 -10 ACMG points.

• BP6: Variant 4-139334493-GA-G is Benign according to our data. Variant chr4-139334493-GA-G is described in ClinVar as [Benign]. Clinvar id is 1296802.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA15	NM_057175.5	c.139+238del		intron_variant		ENST00000296543.10
NAA15	NM_001410842.1	c.139+238del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA15	ENST00000296543.10	c.139+238del		intron_variant		1	NM_057175.5	P3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40336 AN: 151994 Hom.: 5657 Cov.: 22

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.266 AC: 40395 AN: 152112 Hom.: 5677 Cov.: 22 AF XY: 0.261 AC XY: 19430 AN XY: 74354

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.259

Alfa AF: 0.263 Hom.: 657

Bravo AF: 0.266

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs148169780; hg19: chr4-140255647;