rs8187

Positions:

• chr11-34146606-G-A
• chr11-34146606-G-C

Variant summary

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

The NM_024662.3(NAT10):​c.*414G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 156,908 control chromosomes in the GnomAD database, including 2,620 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 0.16 (2514 hom., cov: 33)
  • Exomes 𝑓: 0.17 (106 hom.)
• Consequence: NAT10 NM_024662.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550

Genes affected

NAT10 (HGNC:29830): (N-acetyltransferase 10) The protein encoded by this gene is an RNA cytidine acetyltransferase involved in histone acetylation, tRNA acetylation, the biosynthesis of 18S rRNA, and the enhancement of nuclear architecture and chromatin organization. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAT10	NM_024662.3	c.*414G>A		3_prime_UTR_variant	29/29	ENST00000257829.8	NP_078938.3
NAT10	NM_001144030.2	c.*414G>A		3_prime_UTR_variant	27/27		NP_001137502.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAT10	ENST00000257829.8	c.*414G>A		3_prime_UTR_variant	29/29	1	NM_024662.3	ENSP00000257829	P1
NAT10	ENST00000527971.5	c.*414G>A		3_prime_UTR_variant	8/8	2		ENSP00000437324
NAT10	ENST00000531159.6			downstream_gene_variant		2		ENSP00000433011

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24232 AN: 152056 Hom.: 2518 Cov.: 33

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.173 AC: 817 AN: 4732 Hom.: 106 Cov.: 0 AF XY: 0.176 AC XY: 438 AN XY: 2486

Gnomad4 AFR exome AF: 0.0926

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.361

Gnomad4 SAS exome AF: 0.210

Gnomad4 FIN exome AF: 0.155

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.159 AC: 24223 AN: 152176 Hom.: 2514 Cov.: 33 AF XY: 0.169 AC XY: 12607 AN XY: 74394

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.149

Alfa AF: 0.149 Hom.: 1213

Bravo AF: 0.172

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs8187; hg19: chr11-34168153;