chr7-101172479-A-G

Variant names:

• chr7-101172479-A-G
• rs759287497
• NM_198571.3:c.710T>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_198571.3(NAT16):​c.710T>C​(p.Leu237Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000691 in 1,447,244 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. L237R) 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: 4.49
• 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: Uncertain_significance. The variant received 2 ACMG points.

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

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.710T>C	p.Leu237Pro	missense	Exon 4 of 4	NP_940973.2	Q8N8M0-1
	NAT16	NM_001369694.1		c.710T>C	p.Leu237Pro	missense	Exon 5 of 5	NP_001356623.1	Q8N8M0-1
	NAT16	NM_001369695.1		c.710T>C	p.Leu237Pro	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.710T>C	p.Leu237Pro	missense	Exon 4 of 4	ENSP00000300303.2	Q8N8M0-1
	NAT16	ENST00000455377.5	TSL:1	c.710T>C	p.Leu237Pro	missense	Exon 5 of 5	ENSP00000395125.1	Q8N8M0-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.91e-7 AC: 1 AN: 1447244 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 720074

African (AFR) AF: 0.00 AC: 0 AN: 33042

American (AMR) AF: 0.00 AC: 0 AN: 44034

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25894

East Asian (EAS) AF: 0.00 AC: 0 AN: 39294

South Asian (SAS) AF: 0.0000117 AC: 1 AN: 85206

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44742

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5754

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1109290

Other (OTH) AF: 0.00 AC: 0 AN: 59988

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.24	T
Eigen	Benign	0.12
Eigen_PC	Benign	-0.039
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.066	D
MetaRNN	Uncertain	0.48	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	1.8	L
PhyloP100		4.5
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-4.0	D
REVEL	Uncertain	0.33
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0040	D
Polyphen		1.0	D
Vest4		0.46
MutPred		0.55		Gain of disorder (P = 0.0067)
MVP		0.32
MPC		1.7
ClinPred		0.98	D
GERP RS		1.6
Varity_R		0.63
gMVP		0.75
Mutation Taster		=84/16	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: rs759287497; hg19: chr7-100815760;