rs1041983
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000015.3(NAT2):c.282C>T(p.Tyr94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151710 control chromosomes in the gnomAD Genomes database, including 10194 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 0.36 ( 10194 hom., cov: 31)
Exomes 𝑓: 0.34 ( 15264 hom. )
Consequence
NAT2
NM_000015.3 synonymous
NM_000015.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0750
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP7
?
Synonymous conserved (PhyloP=-0.075 with no splicing effect.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT2 | NM_000015.3 | c.282C>T | p.Tyr94= | synonymous_variant | 2/2 | ENST00000286479.4 | |
NAT2 | XM_017012938.2 | c.282C>T | p.Tyr94= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT2 | ENST00000286479.4 | c.282C>T | p.Tyr94= | synonymous_variant | 2/2 | 1 | NM_000015.3 | P1 | |
NAT2 | ENST00000520116.1 | c.-57-52C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.360 AC: 54604AN: 151710Hom.: 10194 Cov.: 31
GnomAD3 genomes
AF:
AC:
54604
AN:
151710
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
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.342 AC: 85599AN: 250306Hom.: 15264 AF XY: 0.344 AC XY: 46546AN XY: 135260
GnomAD3 exomes
AF:
AC:
85599
AN:
250306
Hom.:
AF XY:
AC XY:
46546
AN XY:
135260
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.328 AC: 479746AN: 1460778Hom.: 80426 AF XY: 0.331 AC XY: 240168AN XY: 726604
GnomAD4 exome
AF:
AC:
479746
AN:
1460778
Hom.:
AF XY:
AC XY:
240168
AN XY:
726604
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1503
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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