Genetic Variant NATP:n.18371679T>C (chr8-18371679-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.104 in 152,224 control chromosomes in the GnomAD database, including 1,009 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 0.10 ( 1009 hom., cov: 33)

Consequence

NATP
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Publications

0 publications found

Variant links:

Genes affected

NATP (HGNC:15): (N-acetyltransferase pseudogene)

NATP 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NATP		n.18371679T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NATP	ENST00000523491.1 link	n.*195T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15791

AN:

152106

Hom.:

1006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0456

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0947

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.104

AC:

15808

AN:

152224

Hom.:

1009

Cov.:

AF XY:

0.107

AC XY:

7946

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0455

AC:

1893

AN:

41562

American (AMR)

AF:

0.186

AC:

2838

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

455

AN:

3464

East Asian (EAS)

AF:

0.146

AC:

754

AN:

5172

South Asian (SAS)

AF:

0.131

AC:

632

AN:

4832

European-Finnish (FIN)

AF:

0.0947

AC:

1006

AN:

10618

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7863

AN:

68000

Other (OTH)

AF:

0.127

AC:

268

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

697

1393

2090

2786

3483

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.108

Hom.:

1057

Bravo

AF:

0.108

Asia WGS

AF:

0.139

AC:

480

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

1.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over