8-123436564-T-G

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F116I) has been classified as Likely benign.

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

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

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
NTAQ1	NM_018024.3	c.346T>G	p.Phe116Val	missense_variant	Exon 4 of 6	ENST00000287387.7	NP_060494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTAQ1	ENST00000287387.7	c.346T>G	p.Phe116Val	missense_variant	Exon 4 of 6	1	NM_018024.3	ENSP00000287387.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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;.;T;T;T
M_CAP	Benign	0.017	T
MetaRNN	Uncertain	0.74	D;D;D;D;D
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.7	M;.;.;.;.
PrimateAI	Uncertain	0.51	T
PROVEAN	Uncertain	-4.4	D;D;.;.;D
REVEL	Benign	0.16
Sift	Benign	0.058	T;T;.;.;T
Sift4G	Benign	0.12	T;T;.;.;T
Polyphen		0.35	B;.;.;.;.
Vest4		0.63
MutPred		0.68		Loss of stability (P = 0.0164);.;.;.;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

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

Publications

LitVar

Other links and lift over

dbSNP: rs6470147; hg19: chr8-124448804;