rs550665110

Variant names:

• chr7-101172389-C-A
• rs550665110
• NM_198571.3:c.800G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-101172389-C-A
• chr7-101172389-C-G
• chr7-101172389-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_198571.3(NAT16):​c.800G>T​(p.Arg267Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000578 in 1,573,232 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00039 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00060 (0 hom.)
• Consequence: NAT16 NM_198571.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0370
• 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0046928525).

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.800G>T	p.Arg267Leu	missense	Exon 4 of 4	NP_940973.2	Q8N8M0-1
	NAT16	NM_001369694.1		c.800G>T	p.Arg267Leu	missense	Exon 5 of 5	NP_001356623.1	Q8N8M0-1
	NAT16	NM_001369695.1		c.800G>T	p.Arg267Leu	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.800G>T	p.Arg267Leu	missense	Exon 4 of 4	ENSP00000300303.2	Q8N8M0-1
	NAT16	ENST00000455377.5	TSL:1	c.800G>T	p.Arg267Leu	missense	Exon 5 of 5	ENSP00000395125.1	Q8N8M0-1

Frequencies

GnomAD3 genomes AF: 0.000394 AC: 60 AN: 152144 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00150

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000426

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000488 AC: 84 AN: 172284 AF XY: 0.000304

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00128

Gnomad ASJ exome AF: 0.000462

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000585

Gnomad OTH exome AF: 0.000850

GnomAD4 exome AF: 0.000597 AC: 849 AN: 1420970 Hom.: 0 Cov.: 33 AF XY: 0.000552 AC XY: 389 AN XY: 704680

African (AFR) AF: 0.000123 AC: 4 AN: 32418

American (AMR) AF: 0.00106 AC: 40 AN: 37904

Ashkenazi Jewish (ASJ) AF: 0.000354 AC: 9 AN: 25428

East Asian (EAS) AF: 0.00 AC: 0 AN: 37346

South Asian (SAS) AF: 0.00 AC: 0 AN: 82912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46034

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5690

European-Non Finnish (NFE) AF: 0.000705 AC: 772 AN: 1094342

Other (OTH) AF: 0.000407 AC: 24 AN: 58896

GnomAD4 genome AF: 0.000394 AC: 60 AN: 152262 Hom.: 1 Cov.: 32 AF XY: 0.000376 AC XY: 28 AN XY: 74462

African (AFR) AF: 0.000168 AC: 7 AN: 41568

American (AMR) AF: 0.00150 AC: 23 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000427 AC: 29 AN: 67990

Other (OTH) AF: 0.00 AC: 0 AN: 2110

Alfa AF: 0.000404 Hom.: 0

Bravo AF: 0.000559

TwinsUK AF: 0.000809 AC: 3

ALSPAC AF: 0.000259 AC: 1

ExAC AF: 0.000258 AC: 30

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.52	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.94
DEOGEN2	Benign	0.0035	T
Eigen	Benign	-0.83
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.18	N
LIST_S2	Benign	0.50	T
M_CAP	Benign	0.0062	T
MetaRNN	Benign	0.0047	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.34	N
PhyloP100		0.037
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	1.5	N
REVEL	Benign	0.046
Sift	Benign	0.68	T
Sift4G	Benign	1.0	T
Polyphen		0.0020	B
Vest4		0.10
MutPred		0.42		Loss of sheet (P = 0.0084)
MVP		0.088
MPC		0.61
ClinPred		0.026	T
GERP RS		0.23
Varity_R		0.054
gMVP		0.35
Mutation Taster		=87/13	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: rs550665110; hg19: chr7-100815670;