chr8-123436564-T-G

Variant names:

• chr8-123436564-T-G
• rs6470147
• NM_018024.3:c.346T>G

Variant summary

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

The NM_018024.3(NTAQ1):​c.346T>G​(p.Phe116Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NTAQ1 NM_018024.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.39
• Publications: 36 publications found

Genes affected

NTAQ1 (HGNC:25490): (N-terminal glutamine amidase 1) Predicted to enable protein-N-terminal glutamine amidohydrolase activity. Predicted to be involved in cellular protein modification process. Predicted to be active in cytosol and nucleus. [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_018024.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTAQ1	NM_018024.3	MANE Select	c.346T>G	p.Phe116Val	missense	Exon 4 of 6	NP_060494.1
	NTAQ1	NM_001283024.1		c.166T>G	p.Phe56Val	missense	Exon 4 of 6	NP_001269953.1
	NTAQ1	NM_001283027.1		c.142T>G	p.Phe48Val	missense	Exon 5 of 7	NP_001269956.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTAQ1	ENST00000287387.7	TSL:1 MANE Select	c.346T>G	p.Phe116Val	missense	Exon 4 of 6	ENSP00000287387.2
	NTAQ1	ENST00000523356.1	TSL:3	c.346T>G	p.Phe116Val	missense	Exon 4 of 7	ENSP00000428615.1
	NTAQ1	ENST00000650311.1		c.166T>G	p.Phe56Val	missense	Exon 4 of 7	ENSP00000497747.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Benign	-0.018	T
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	24
DANN	Uncertain	0.98
DEOGEN2	Benign	0.074	T
Eigen	Benign	0.13
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.017	T
MetaRNN	Uncertain	0.74	D
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.7	M
PhyloP100		3.4
PrimateAI	Uncertain	0.51	T
PROVEAN	Uncertain	-4.4	D
REVEL	Benign	0.16
Sift	Benign	0.058	T
Sift4G	Benign	0.12	T
Polyphen		0.35	B
Vest4		0.63
MutPred		0.68		Loss of stability (P = 0.0164)
MVP		0.26
MPC		0.20
ClinPred		0.99	D
GERP RS		4.4
Varity_R		0.36
gMVP		0.57
Mutation Taster		=83/17	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6470147; hg19: chr8-124448804;