7-101172144-C-T

Variant names:

• chr7-101172144-C-T
• rs1797337346
• NM_198571.3:c.1045G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198571.3(NAT16):​c.1045G>A​(p.Val349Ile) 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. 16/22 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. V349L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NAT16 NM_198571.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.031181127).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198571.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT16	NM_198571.3	MANE Select	c.1045G>A	p.Val349Ile	missense	Exon 4 of 4	NP_940973.2	Q8N8M0-1
	NAT16	NM_001369694.1		c.1045G>A	p.Val349Ile	missense	Exon 5 of 5	NP_001356623.1	Q8N8M0-1
	NAT16	NM_001369695.1		c.1045G>A	p.Val349Ile	missense	Exon 4 of 4	NP_001356624.1	Q8N8M0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT16	ENST00000300303.7	TSL:2 MANE Select	c.1045G>A	p.Val349Ile	missense	Exon 4 of 4	ENSP00000300303.2	Q8N8M0-1
	NAT16	ENST00000455377.5	TSL:1	c.1045G>A	p.Val349Ile	missense	Exon 5 of 5	ENSP00000395125.1	Q8N8M0-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.93
DEOGEN2	Benign	0.0079	T
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.67
FATHMM_MKL	Benign	0.062	N
LIST_S2	Benign	0.33	T
M_CAP	Benign	0.0075	T
MetaRNN	Benign	0.031	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.21
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.30	N
REVEL	Benign	0.030
Sift	Benign	0.20	T
Sift4G	Benign	0.23	T
Polyphen		0.020	B
Vest4		0.058
MutPred		0.28		Loss of sheet (P = 0.0315)
MVP		0.067
MPC		0.40
ClinPred		0.096	T
GERP RS		3.0
Varity_R		0.066
gMVP		0.060
Mutation Taster		=99/1	polymorphism

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

Other links and lift over

dbSNP: rs1797337346; hg19: chr7-100815425;