rs4980499

chr11-63939731-G-A

Variant summary

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

The NM_024771.4(NAA40):c.6+629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,076 control chromosomes in the GnomAD database, including 7,374 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 0.27 (7374 hom., cov: 31)
• Consequence: NAA40 NM_024771.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

Genes affected

NAA40 (HGNC:25845): (N-alpha-acetyltransferase 40, NatD catalytic subunit) Enables H2A histone acetyltransferase activity; H4 histone acetyltransferase activity; and peptide-serine-N-acetyltransferase activity. Involved in N-terminal protein amino acid acetylation; histone H2A acetylation; and histone H4 acetylation. Located in centriolar satellite; cytosol; and nucleoplasm. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAA40	NM_024771.4	c.6+629G>A		intron_variant		ENST00000377793.9
NAA40	NM_001300800.1	c.-58+197G>A		intron_variant
NAA40	XM_006718689.4	c.6+629G>A		intron_variant
NAA40	XM_011545254.3	c.-171+629G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA40	ENST00000377793.9	c.6+629G>A		intron_variant		1	NM_024771.4	P1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41807 AN: 151958 Hom.: 7367 Cov.: 31

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.275 AC: 41817 AN: 152076 Hom.: 7374 Cov.: 31 AF XY: 0.274 AC XY: 20373 AN XY: 74304

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.280

Alfa AF: 0.320 Hom.: 1447

Bravo AF: 0.249

Asia WGS AF: 0.146 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.51
Dann	Benign	0.48

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: rs4980499; hg19: chr11-63707203;