dbSNP rs8187: NAT10:c.*414G>A (chr11-34146606-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.550

Publications

10 publications found

Variant links:

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]

NAT10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT10	NM_024662.3 link	c.*414G>A		3_prime_UTR_variant	Exon 29 of 29	ENST00000257829.8	NP_078938.3	Q9H0A0-1
NAT10	NM_001144030.2 link	c.*414G>A		3_prime_UTR_variant	Exon 27 of 27		NP_001137502.2	Q9H0A0-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
NAT10	ENST00000257829.8 link	c.*414G>A	3_prime_UTR_variant	Exon 29 of 29	1	NM_024662.3	ENSP00000257829.3	Q9H0A0-1
NAT10	ENST00000527971.5 link	c.*414G>A	3_prime_UTR_variant	Exon 8 of 8	2		ENSP00000437324.1	E9PMU0
NAT10	ENST00000534509.1 link	n.-114G>A	upstream_gene_variant		3
NAT10	ENST00000531159.6 link	c.*414G>A	downstream_gene_variant		2		ENSP00000433011.2	Q9H0A0-2

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24232

AN:

152056

Hom.:

2518

Cov.:

show subpopulations

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.:

AF XY:

0.176

AC XY:

438

AN XY:

2486

show subpopulations

African (AFR)

AF:

0.0926

AC:

AN:

American (AMR)

AF:

0.353

AC:

290

AN:

822

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

AN:

East Asian (EAS)

AF:

0.361

AC:

AN:

108

South Asian (SAS)

AF:

0.210

AC:

AN:

442

European-Finnish (FIN)

AF:

0.155

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.114

AC:

335

AN:

2926

Other (OTH)

AF:

0.149

AC:

AN:

228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

117

146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.159

AC:

24223

AN:

152176

Hom.:

2514

Cov.:

AF XY:

0.169

AC XY:

12607

AN XY:

74394

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9072

AN:

68010

Other (OTH)

AF:

0.149

AC:

314

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1028

2056

3085

4113

5141

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.0

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over