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GeneBe

rs1801280

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2_SupportingPP3_Strong

The NM_000015.3(NAT2):c.341T>A(p.Ile114Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000659 in 151644 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I114T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 29)

Consequence

NAT2
NM_000015.3 missense

Scores

4
3
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.86

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.00000659 (1/151644) while in subpopulation NFE AF= 0.0000147 (1/67944). AF 95% confidence interval is 0. There are 0 homozygotes in gnomad. There are 1 alleles in male gnomad subpopulation. Median coverage is 29. This position pass quality control queck.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.972

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAT2NM_000015.3 linkuse as main transcriptc.341T>A p.Ile114Asn missense_variant 2/2 ENST00000286479.4
NAT2XM_017012938.2 linkuse as main transcriptc.341T>A p.Ile114Asn missense_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAT2ENST00000286479.4 linkuse as main transcriptc.341T>A p.Ile114Asn missense_variant 2/21 NM_000015.3 P1
NAT2ENST00000520116.1 linkuse as main transcriptc.-50T>A 5_prime_UTR_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151644
Hom.:
0
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461042
Hom.:
0
AF XY:
0.00000138
AC XY:
1
AN XY:
726794
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
Cadd
Benign
23
Dann
Uncertain
0.99
Eigen
Benign
0.12
Eigen_PC
Benign
-0.15
FATHMM_MKL
Uncertain
0.81
D
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.0056
T
MetaRNN
Pathogenic
0.97
D
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
0.85
N;N
PrimateAI
Benign
0.40
T
PROVEAN
Pathogenic
-6.2
D
REVEL
Benign
0.091
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0010
D
Polyphen
1.0
D
Vest4
0.76
MutPred
0.81
Loss of stability (P = 0.0289);
MVP
0.37
MPC
0.015
ClinPred
1.0
D
GERP RS
0.54
gMVP
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1801280; hg19: chr8-18257854; API