rs2410556

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000015.3(NAT2):​c.-6-3041T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,246 control chromosomes in the GnomAD database, including 910 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 0.094 ( 910 hom., cov: 33)

Consequence

NAT2
NM_000015.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.295
Variant links:
Genes affected
NAT2 (HGNC:7646): (N-acetyltransferase 2) This gene encodes an enzyme that functions to both activate and deactivate arylamine and hydrazine drugs and carcinogens. Polymorphisms in this gene are responsible for the N-acetylation polymorphism in which human populations segregate into rapid, intermediate, and slow acetylator phenotypes. Polymorphisms in this gene are also associated with higher incidences of cancer and drug toxicity. A second polymorphic arylamine N-acetyltransferase gene (NAT1), is located near this gene (NAT2). [provided by RefSeq, Sep 2019]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAT2NM_000015.3 linkuse as main transcriptc.-6-3041T>C intron_variant ENST00000286479.4
NAT2XM_017012938.2 linkuse as main transcriptc.-6-3041T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAT2ENST00000286479.4 linkuse as main transcriptc.-6-3041T>C intron_variant 1 NM_000015.3 P1
NAT2ENST00000520116.1 linkuse as main transcriptc.-57-3380T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0936
AC:
14242
AN:
152128
Hom.:
910
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0251
Gnomad AMI
AF:
0.0735
Gnomad AMR
AF:
0.102
Gnomad ASJ
AF:
0.178
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0286
Gnomad FIN
AF:
0.120
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.137
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0935
AC:
14238
AN:
152246
Hom.:
910
Cov.:
33
AF XY:
0.0907
AC XY:
6752
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0250
Gnomad4 AMR
AF:
0.102
Gnomad4 ASJ
AF:
0.178
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0284
Gnomad4 FIN
AF:
0.120
Gnomad4 NFE
AF:
0.135
Gnomad4 OTH
AF:
0.136
Alfa
AF:
0.135
Hom.:
1458
Bravo
AF:
0.0913
Asia WGS
AF:
0.0140
AC:
49
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.7
DANN
Benign
0.72

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2410556; hg19: chr8-18254467; API