dbSNP rs1879662: NAT8:c.*175T>C (chr2-73640770-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003960.4(NAT8):c.*175T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 629,454 control chromosomes in the GnomAD database, including 231,816 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 0.87 ( 57239 hom., cov: 33)

Exomes 𝑓: 0.85 ( 174577 hom. )

Consequence

NAT8
NM_003960.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.547

Publications

5 publications found

Variant links:

Genes affected

NAT8 (HGNC:18069): (N-acetyltransferase 8 (putative)) This gene, isolated using the differential display method to detect tissue-specific genes, is specifically expressed in kidney and liver. The encoded protein shows amino acid sequence similarity to N-acetyltransferases. A similar protein in Xenopus affects cell adhesion and gastrulation movements, and may be localized in the secretory pathway. A highly similar paralog is found in a cluster with this gene. [provided by RefSeq, Sep 2008]

NAT8 links:

ALMS1P1 (HGNC:):

ALMS1P1 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003960.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT8	NM_003960.4	MANE Select	c.*175T>C		3_prime_UTR	Exon 2 of 2	NP_003951.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NAT8	ENST00000272425.4	TSL:1 MANE Select	c.*175T>C	3_prime_UTR	Exon 2 of 2	ENSP00000272425.3	Q9UHE5
ALMS1P1	ENST00000755941.1		n.48A>G	non_coding_transcript_exon	Exon 1 of 6
NAT8	ENST00000852385.1		c.*175T>C	downstream_gene	N/A	ENSP00000522444.1

Frequencies

GnomAD3 genomes

AF:

0.866

AC:

131711

AN:

152110

Hom.:

57191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.958

Gnomad AMR

AF:

0.917

Gnomad ASJ

AF:

0.816

Gnomad EAS

AF:

0.679

Gnomad SAS

AF:

0.823

Gnomad FIN

AF:

0.851

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.870

Gnomad OTH

AF:

0.869

GnomAD4 exome

AF:

0.853

AC:

407202

AN:

477226

Hom.:

174577

AF XY:

0.853

AC XY:

206498

AN XY:

242102

show subpopulations

African (AFR)

AF:

0.865

AC:

11743

AN:

13572

American (AMR)

AF:

0.935

AC:

14983

AN:

16018

Ashkenazi Jewish (ASJ)

AF:

0.824

AC:

10619

AN:

12886

East Asian (EAS)

AF:

0.670

AC:

20479

AN:

30548

South Asian (SAS)

AF:

0.830

AC:

21756

AN:

26198

European-Finnish (FIN)

AF:

0.849

AC:

24843

AN:

29262

Middle Eastern (MID)

AF:

0.847

AC:

1684

AN:

1988

European-Non Finnish (NFE)

AF:

0.869

AC:

278499

AN:

320498

Other (OTH)

AF:

0.861

AC:

22596

AN:

26256

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2846

5692

8539

11385

14231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3076

6152

9228

12304

15380

<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:

0.866

AC:

131818

AN:

152228

Hom.:

57239

Cov.:

AF XY:

0.865

AC XY:

64387

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.875

AC:

36373

AN:

41560

American (AMR)

AF:

0.917

AC:

13985

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.816

AC:

2834

AN:

3472

East Asian (EAS)

AF:

0.679

AC:

3511

AN:

5170

South Asian (SAS)

AF:

0.824

AC:

3975

AN:

4826

European-Finnish (FIN)

AF:

0.851

AC:

9033

AN:

10610

Middle Eastern (MID)

AF:

0.864

AC:

254

AN:

294

European-Non Finnish (NFE)

AF:

0.870

AC:

59152

AN:

68022

Other (OTH)

AF:

0.866

AC:

1829

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

902

1804

2705

3607

4509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

896

1792

2688

3584

4480

<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:

0.872

Hom.:

7193

Bravo

AF:

0.870

Asia WGS

AF:

0.776

AC:

2698

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.5

(source)

DANN

Benign

0.69

PhyloP100

0.55

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over