rs4980499

Variant names:

• chr11-63939731-G-A
• rs4980499
• NM_024771.4:c.6+629G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NAA40	NM_024771.4	c.6+629G>A		intron_variant	Intron 1 of 7	ENST00000377793.9	NP_079047.2
NAA40	NM_001300800.1	c.-58+197G>A		intron_variant	Intron 1 of 7		NP_001287729.1
NAA40	XM_006718689.4	c.6+629G>A		intron_variant	Intron 1 of 7		XP_006718752.1
NAA40	XM_011545254.3	c.-171+629G>A		intron_variant	Intron 1 of 8		XP_011543556.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAA40	ENST00000377793.9	c.6+629G>A		intron_variant	Intron 1 of 7	1	NM_024771.4	ENSP00000367024.4

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

African (AFR) AF: 0.0744 AC: 3089 AN: 41532

American (AMR) AF: 0.222 AC: 3393 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3468

East Asian (EAS) AF: 0.0470 AC: 243 AN: 5168

South Asian (SAS) AF: 0.314 AC: 1512 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4345 AN: 10548

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26622 AN: 67956

Other (OTH) AF: 0.280 AC: 591 AN: 2110

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
PhyloP100		-0.85
PromoterAI		0.026	Neutral
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: rs4980499; hg19: chr11-63707203;