NM_198571.3:c.749G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_198571.3(NAT16):​c.749G>C​(p.Arg250Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000563 in 1,597,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign 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. R250Q) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.000013 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000048 ( 0 hom. )

Consequence

NAT16
NM_198571.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.384
Variant links:
Genes affected
NAT16 (HGNC:22030): (N-acetyltransferase 16 (putative)) Predicted to enable acyltransferase activity, transferring groups other than amino-acyl groups. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03675255).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAT16NM_198571.3 linkc.749G>C p.Arg250Pro missense_variant Exon 4 of 4 ENST00000300303.7 NP_940973.2 Q8N8M0-1
NAT16NM_001369694.1 linkc.749G>C p.Arg250Pro missense_variant Exon 5 of 5 NP_001356623.1
NAT16NM_001369695.1 linkc.749G>C p.Arg250Pro missense_variant Exon 4 of 4 NP_001356624.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NAT16ENST00000300303.7 linkc.749G>C p.Arg250Pro missense_variant Exon 4 of 4 2 NM_198571.3 ENSP00000300303.2 Q8N8M0-1
NAT16ENST00000455377.5 linkc.749G>C p.Arg250Pro missense_variant Exon 5 of 5 1 ENSP00000395125.1 Q8N8M0-1

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152168
Hom.:
0
Cov.:
32
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:
0.000386
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000922
AC:
2
AN:
216850
Hom.:
0
AF XY:
0.00000835
AC XY:
1
AN XY:
119782
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000600
Gnomad SAS exome
AF:
0.0000349
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000484
AC:
7
AN:
1445268
Hom.:
0
Cov.:
33
AF XY:
0.00000417
AC XY:
3
AN XY:
718680
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000511
Gnomad4 SAS exome
AF:
0.0000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000271
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152286
Hom.:
0
Cov.:
32
AF XY:
0.0000269
AC XY:
2
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.00000834
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.020
T;T
Eigen
Benign
-0.85
Eigen_PC
Benign
-0.87
FATHMM_MKL
Benign
0.53
D
LIST_S2
Benign
0.79
.;T
M_CAP
Benign
0.0058
T
MetaRNN
Benign
0.037
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.1
L;L
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-1.4
N;N
REVEL
Benign
0.051
Sift
Benign
0.067
T;T
Sift4G
Uncertain
0.024
D;D
Polyphen
0.0060
B;B
Vest4
0.38
MutPred
0.35
Gain of glycosylation at R250 (P = 0.009);Gain of glycosylation at R250 (P = 0.009);
MVP
0.048
MPC
1.4
ClinPred
0.44
T
GERP RS
-4.8
Varity_R
0.28
gMVP
0.65

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: rs551457672; hg19: chr7-100815721; API