rs762062727

Variant names:

• chr7-101173360-C-A
• rs762062727
• NM_198571.3:c.473G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-101173360-C-A
• chr7-101173360-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_198571.3(NAT16):​c.473G>T​(p.Arg158Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. R158Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NAT16 NM_198571.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

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 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.37004972).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT16	NM_198571.3	c.473G>T	p.Arg158Leu	missense_variant	Exon 3 of 4	ENST00000300303.7	NP_940973.2
NAT16	NM_001369694.1	c.473G>T	p.Arg158Leu	missense_variant	Exon 4 of 5		NP_001356623.1
NAT16	NM_001369695.1	c.473G>T	p.Arg158Leu	missense_variant	Exon 3 of 4		NP_001356624.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAT16	ENST00000300303.7	c.473G>T	p.Arg158Leu	missense_variant	Exon 3 of 4	2	NM_198571.3	ENSP00000300303.2
NAT16	ENST00000455377.5	c.473G>T	p.Arg158Leu	missense_variant	Exon 4 of 5	1		ENSP00000395125.1
NAT16	ENST00000444446.1	c.*4G>T		downstream_gene_variant		4		ENSP00000391769.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Benign	0.25	T;T
Eigen	Benign	-0.60
Eigen_PC	Benign	-0.72
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.73	.;T
M_CAP	Benign	0.0082	T
MetaRNN	Benign	0.37	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.8	M;M
PrimateAI	Benign	0.27	T
PROVEAN	Uncertain	-4.2	D;D
REVEL	Benign	0.15
Sift	Uncertain	0.0070	D;D
Sift4G	Uncertain	0.016	D;D
Polyphen		0.38	B;B
Vest4		0.62
MutPred		0.56		Loss of MoRF binding (P = 0.0072);Loss of MoRF binding (P = 0.0072);
MVP		0.13
MPC		0.74
ClinPred		0.97	D
GERP RS		-0.71
Varity_R		0.20
gMVP		0.69

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

Other links and lift over

dbSNP: rs762062727; hg19: chr7-100816641;