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GeneBe

rs1799929

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000015.3(NAT2):c.481C>T(p.Leu161=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151434 control chromosomes in the gnomAD Genomes database, including 10488 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 ( 10488 hom., cov: 29)
Exomes 𝑓: 0.36 ( 18050 hom. )

Consequence

NAT2
NM_000015.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00900

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP7
?
Synonymous conserved (PhyloP=0.009 with no splicing effect.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAT2NM_000015.3 linkuse as main transcriptc.481C>T p.Leu161= synonymous_variant 2/2 ENST00000286479.4
NAT2XM_017012938.2 linkuse as main transcriptc.481C>T p.Leu161= synonymous_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAT2ENST00000286479.4 linkuse as main transcriptc.481C>T p.Leu161= synonymous_variant 2/21 NM_000015.3 P1
NAT2ENST00000520116.1 linkuse as main transcriptc.91C>T p.Leu31= synonymous_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.358
AC:
54155
AN:
151434
Hom.:
10488
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.338
Gnomad AMR
AF:
0.339
Gnomad ASJ
AF:
0.435
Gnomad EAS
AF:
0.0362
Gnomad SAS
AF:
0.306
Gnomad FIN
AF:
0.443
Gnomad MID
AF:
0.434
Gnomad NFE
AF:
0.431
Gnomad OTH
AF:
0.375
GnomAD3 exomes
AF:
0.361
AC:
90469
AN:
250414
Hom.:
18050
AF XY:
0.366
AC XY:
49605
AN XY:
135422
show subpopulations
Gnomad AFR exome
AF:
0.257
Gnomad AMR exome
AF:
0.299
Gnomad ASJ exome
AF:
0.439
Gnomad EAS exome
AF:
0.0383
Gnomad SAS exome
AF:
0.310
Gnomad FIN exome
AF:
0.438
Gnomad NFE exome
AF:
0.438
Gnomad OTH exome
AF:
0.397
GnomAD4 exome
AF:
0.408
AC:
596117
AN:
1461166
Hom.:
126442
AF XY:
0.407
AC XY:
295485
AN XY:
726878
show subpopulations
Gnomad4 AFR exome
AF:
0.261
Gnomad4 AMR exome
AF:
0.305
Gnomad4 ASJ exome
AF:
0.433
Gnomad4 EAS exome
AF:
0.0271
Gnomad4 SAS exome
AF:
0.309
Gnomad4 FIN exome
AF:
0.434
Gnomad4 NFE exome
AF:
0.437
Gnomad4 OTH exome
AF:
0.391
Alfa
AF:
0.412
Hom.:
33505
Bravo
AF:
0.346
Asia WGS
AF:
0.178
AC:
620
AN:
3478
EpiCase
AF:
0.431
EpiControl
AF:
0.429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
Cadd
Benign
5.5
Dann
Benign
0.55

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: rs1799929; hg19: chr8-18257994; COSMIC: COSV54061442; API