11-34146606-G-A

Variant names:

• chr11-34146606-G-A
• rs8187
• NM_024662.3:c.*414G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024662.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT10	NM_024662.3	MANE Select	c.*414G>A		3_prime_UTR	Exon 29 of 29	NP_078938.3
	NAT10	NM_001144030.2		c.*414G>A		3_prime_UTR	Exon 27 of 27	NP_001137502.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT10	ENST00000257829.8	TSL:1 MANE Select	c.*414G>A		3_prime_UTR	Exon 29 of 29	ENSP00000257829.3
	NAT10	ENST00000527971.5	TSL:2	c.*414G>A		3_prime_UTR	Exon 8 of 8	ENSP00000437324.1
	NAT10	ENST00000534509.1	TSL:3	n.-114G>A		upstream_gene	N/A

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

African (AFR) AF: 0.0926 AC: 5 AN: 54

American (AMR) AF: 0.353 AC: 290 AN: 822

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 8 AN: 64

East Asian (EAS) AF: 0.361 AC: 39 AN: 108

South Asian (SAS) AF: 0.210 AC: 93 AN: 442

European-Finnish (FIN) AF: 0.155 AC: 13 AN: 84

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.114 AC: 335 AN: 2926

Other (OTH) AF: 0.149 AC: 34 AN: 228

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

African (AFR) AF: 0.0961 AC: 3991 AN: 41528

American (AMR) AF: 0.313 AC: 4780 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2011 AN: 5166

South Asian (SAS) AF: 0.274 AC: 1322 AN: 4818

European-Finnish (FIN) AF: 0.189 AC: 1998 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9072 AN: 68010

Other (OTH) AF: 0.149 AC: 314 AN: 2108

Alfa AF: 0.149 Hom.: 1290

Bravo AF: 0.172

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs8187; hg19: chr11-34168153;