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GeneBe

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

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
NAT2NM_000015.3 linkuse as main transcriptc.282C>T p.Tyr94= synonymous_variant 2/2 ENST00000286479.4
NAT2XM_017012938.2 linkuse as main transcriptc.282C>T p.Tyr94= synonymous_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAT2ENST00000286479.4 linkuse as main transcriptc.282C>T p.Tyr94= synonymous_variant 2/21 NM_000015.3 P1
NAT2ENST00000520116.1 linkuse as main transcriptc.-57-52C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.360
AC:
54604
AN:
151710
Hom.:
10194
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.450
Gnomad AMI
AF:
0.355
Gnomad AMR
AF:
0.321
Gnomad ASJ
AF:
0.382
Gnomad EAS
AF:
0.412
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.267
Gnomad MID
AF:
0.334
Gnomad NFE
AF:
0.318
Gnomad OTH
AF:
0.362
GnomAD3 exomes
AF:
0.342
AC:
85599
AN:
250306
Hom.:
15264
AF XY:
0.344
AC XY:
46546
AN XY:
135260
show subpopulations
Gnomad AFR exome
AF:
0.449
Gnomad AMR exome
AF:
0.304
Gnomad ASJ exome
AF:
0.372
Gnomad EAS exome
AF:
0.419
Gnomad SAS exome
AF:
0.428
Gnomad FIN exome
AF:
0.274
Gnomad NFE exome
AF:
0.313
Gnomad OTH exome
AF:
0.330
GnomAD4 exome
AF:
0.328
AC:
479746
AN:
1460778
Hom.:
80426
AF XY:
0.331
AC XY:
240168
AN XY:
726604
show subpopulations
Gnomad4 AFR exome
AF:
0.455
Gnomad4 AMR exome
AF:
0.307
Gnomad4 ASJ exome
AF:
0.382
Gnomad4 EAS exome
AF:
0.352
Gnomad4 SAS exome
AF:
0.428
Gnomad4 FIN exome
AF:
0.278
Gnomad4 NFE exome
AF:
0.317
Gnomad4 OTH exome
AF:
0.347
Alfa
AF:
0.327
Hom.:
17518
Bravo
AF:
0.363
Asia WGS
AF:
0.432
AC:
1503
AN:
3478
EpiCase
AF:
0.319
EpiControl
AF:
0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
0.77
Dann
Benign
0.28

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: rs1041983; hg19: chr8-18257795; COSMIC: COSV54061508;