rs8190862
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000662.8(NAT1):c.*472C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 167,152 control chromosomes in the GnomAD database, including 50 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 0.018 ( 49 hom., cov: 32)
Exomes 𝑓: 0.0086 ( 1 hom. )
Consequence
NAT1
NM_000662.8 3_prime_UTR
NM_000662.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.81
Publications
5 publications found
Genes affected
NAT1 (HGNC:7645): (N-acetyltransferase 1) This gene is one of two arylamine N-acetyltransferase (NAT) genes in the human genome, and is orthologous to the mouse and rat Nat2 genes. The enzyme encoded by this gene catalyzes the transfer of an acetyl group from acetyl-CoA to various arylamine and hydrazine substrates. This enzyme helps metabolize drugs and other xenobiotics, and functions in folate catabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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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=-0.95).
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0182 (2764/152260) while in subpopulation SAS AF = 0.0363 (175/4822). AF 95% confidence interval is 0.0319. There are 49 homozygotes in GnomAd4. There are 1300 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 2764 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 2756AN: 152142Hom.: 49 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2756
AN:
152142
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00860 AC: 128AN: 14892Hom.: 1 Cov.: 0 AF XY: 0.0102 AC XY: 72AN XY: 7080 show subpopulations
GnomAD4 exome
AF:
AC:
128
AN:
14892
Hom.:
Cov.:
0
AF XY:
AC XY:
72
AN XY:
7080
show subpopulations
African (AFR)
AF:
AC:
0
AN:
4
American (AMR)
AF:
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
6
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
121
AN:
14684
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
6
AN:
102
Other (OTH)
AF:
AC:
1
AN:
90
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.473
Heterozygous variant carriers
0
8
15
23
30
38
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0182 AC: 2764AN: 152260Hom.: 49 Cov.: 32 AF XY: 0.0175 AC XY: 1300AN XY: 74452 show subpopulations
GnomAD4 genome
AF:
AC:
2764
AN:
152260
Hom.:
Cov.:
32
AF XY:
AC XY:
1300
AN XY:
74452
show subpopulations
African (AFR)
AF:
AC:
204
AN:
41564
American (AMR)
AF:
AC:
225
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
146
AN:
3468
East Asian (EAS)
AF:
AC:
34
AN:
5186
South Asian (SAS)
AF:
AC:
175
AN:
4822
European-Finnish (FIN)
AF:
AC:
94
AN:
10604
Middle Eastern (MID)
AF:
AC:
25
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1738
AN:
68006
Other (OTH)
AF:
AC:
49
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
137
274
412
549
686
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
36
72
108
144
180
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
83
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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