rs879584444

Variant names:

• chr7-101172582-G-A
• NM_198571.3:c.607C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-101172582-G-A
• chr7-101172582-G-C
• chr7-101172582-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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]

ACMG classification

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
NAT16	NM_198571.3	c.607C>T	p.Arg203Trp	missense_variant	Exon 4 of 4	ENST00000300303.7	NP_940973.2
NAT16	NM_001369694.1	c.607C>T	p.Arg203Trp	missense_variant	Exon 5 of 5		NP_001356623.1
NAT16	NM_001369695.1	c.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
NAT16	ENST00000300303.7	c.607C>T	p.Arg203Trp	missense_variant	Exon 4 of 4	2	NM_198571.3	ENSP00000300303.2
NAT16	ENST00000455377.5	c.607C>T	p.Arg203Trp	missense_variant	Exon 5 of 5	1		ENSP00000395125.1

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

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;