rs201313983

Variant names:

• chr7-101172092-T-A
• NM_198571.3:c.1097A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-101172092-T-A
• chr7-101172092-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_198571.3(NAT16):​c.1097A>T​(p.Glu366Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,660 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. E366G) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: NAT16 NM_198571.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.98

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT16	NM_198571.3	c.1097A>T	p.Glu366Val	missense_variant	Exon 4 of 4	ENST00000300303.7	NP_940973.2
NAT16	NM_001369694.1	c.1097A>T	p.Glu366Val	missense_variant	Exon 5 of 5		NP_001356623.1
NAT16	NM_001369695.1	c.1097A>T	p.Glu366Val	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.1097A>T	p.Glu366Val	missense_variant	Exon 4 of 4	2	NM_198571.3	ENSP00000300303.2
NAT16	ENST00000455377.5	c.1097A>T	p.Glu366Val	missense_variant	Exon 5 of 5	1		ENSP00000395125.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1458660 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 725584

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: 9.01e-7

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	Pathogenic	0.97
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.32	T;T
Eigen	Uncertain	0.38
Eigen_PC	Uncertain	0.33
FATHMM_MKL	Benign	0.73	D
LIST_S2	Benign	0.53	.;T
M_CAP	Uncertain	0.13	D
MetaRNN	Uncertain	0.53	D;D
MetaSVM	Benign	-0.58	T
MutationAssessor	Benign	1.8	L;L
PrimateAI	Benign	0.38	T
PROVEAN	Uncertain	-3.6	D;D
REVEL	Uncertain	0.39
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.48
MutPred		0.40		Loss of disorder (P = 0.0012);Loss of disorder (P = 0.0012);
MVP		0.43
MPC		1.5
ClinPred		1.0	D
GERP RS		3.2
Varity_R		0.76
gMVP		0.62

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: chr7-100815373;