rs8190865
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000662.8(NAT1):c.*769A>C variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 129,410 control chromosomes in the GnomAD database, including 38 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 0.012 ( 38 hom., cov: 31)
Exomes 𝑓: 0.00066 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NAT1
NM_000662.8 splice_region
NM_000662.8 splice_region
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.406
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=-0.99).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0123 (1586/129410) while in subpopulation AFR AF = 0.0396 (1508/38044). AF 95% confidence interval is 0.038. There are 38 homozygotes in GnomAd4. There are 735 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position FAILED quality control check.
BS2
High AC in GnomAd4 at 1586 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1590AN: 129282Hom.: 38 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1590
AN:
129282
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000665 AC: 5AN: 7520Hom.: 0 Cov.: 0 AF XY: 0.000554 AC XY: 2AN XY: 3612 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
5
AN:
7520
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
3612
Gnomad4 AFR exome
AF:
AC:
0
AN:
4
Gnomad4 AMR exome
AF:
AC:
0
AN:
4
Gnomad4 ASJ exome
AC:
0
AN:
0
Gnomad4 EAS exome
AC:
0
AN:
0
Gnomad4 SAS exome
AC:
0
AN:
0
Gnomad4 FIN exome
AF:
AC:
5
AN:
7400
Gnomad4 NFE exome
AF:
AC:
0
AN:
62
Gnomad4 Remaining exome
AF:
AC:
0
AN:
50
⚠️ The allele balance in gnomAD4 Exomes is highly skewed (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0123 AC: 1586AN: 129410Hom.: 38 Cov.: 31 AF XY: 0.0117 AC XY: 735AN XY: 62906 show subpopulations
GnomAD4 genome
AF:
AC:
1586
AN:
129410
Hom.:
Cov.:
31
AF XY:
AC XY:
735
AN XY:
62906
Gnomad4 AFR
AF:
AC:
0.0396383
AN:
0.0396383
Gnomad4 AMR
AF:
AC:
0.00310835
AN:
0.00310835
Gnomad4 ASJ
AF:
AC:
0.000359454
AN:
0.000359454
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.000260552
AN:
0.000260552
Gnomad4 FIN
AF:
AC:
0.000138581
AN:
0.000138581
Gnomad4 NFE
AF:
AC:
0.00035572
AN:
0.00035572
Gnomad4 OTH
AF:
AC:
0.00715072
AN:
0.00715072
Heterozygous variant carriers
0
67
134
200
267
334
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
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55-60
60-65
65-70
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75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at