rs879584444

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_198571.3(NAT16):​c.607C>T​(p.Arg203Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000725 in 1,379,162 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. R203G) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.3e-7 ( 0 hom. )

Consequence

NAT16
NM_198571.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07081428).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAT16NM_198571.3 linkc.607C>T p.Arg203Trp missense_variant Exon 4 of 4 ENST00000300303.7 NP_940973.2 Q8N8M0-1
NAT16NM_001369694.1 linkc.607C>T p.Arg203Trp missense_variant Exon 5 of 5 NP_001356623.1
NAT16NM_001369695.1 linkc.607C>T p.Arg203Trp 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.607C>T p.Arg203Trp missense_variant Exon 4 of 4 2 NM_198571.3 ENSP00000300303.2 Q8N8M0-1
NAT16ENST00000455377.5 linkc.607C>T p.Arg203Trp missense_variant Exon 5 of 5 1 ENSP00000395125.1 Q8N8M0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.25e-7
AC:
1
AN:
1379162
Hom.:
0
Cov.:
34
AF XY:
0.00000147
AC XY:
1
AN XY:
682164
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000289
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
8.8
DANN
Uncertain
0.99
DEOGEN2
Benign
0.026
T;T
Eigen
Benign
-0.96
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.040
N
LIST_S2
Benign
0.60
.;T
M_CAP
Benign
0.0046
T
MetaRNN
Benign
0.071
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N
PrimateAI
Uncertain
0.64
T
PROVEAN
Benign
-2.1
N;N
REVEL
Benign
0.020
Sift
Uncertain
0.021
D;D
Sift4G
Benign
0.067
T;T
Polyphen
0.0040
B;B
Vest4
0.14
MutPred
0.34
Loss of disorder (P = 0.0116);Loss of disorder (P = 0.0116);
MVP
0.040
MPC
0.52
ClinPred
0.28
T
GERP RS
1.1
Varity_R
0.062
gMVP
0.38

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-100815863; API