8-123436564-TTT-GTA

Variant names:

• chr8-123436564-TTT-GTA
• NM_018024.3:c.346_348delTTTinsGTA
• NTAQ1 p.Phe116Val

Variant summary

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

The NM_018024.3(NTAQ1):​c.346_348delTTTinsGTA​(p.Phe116Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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: 6.08
• Publications: 0 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 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTAQ1	NM_018024.3	MANE Select	c.346_348delTTTinsGTA	p.Phe116Val	missense	N/A	NP_060494.1	Q96HA8-1
	NTAQ1	NM_001283024.1		c.166_168delTTTinsGTA	p.Phe56Val	missense	N/A	NP_001269953.1	Q96HA8-2
	NTAQ1	NM_001283027.1		c.142_144delTTTinsGTA	p.Phe48Val	missense	N/A	NP_001269956.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTAQ1	ENST00000287387.7	TSL:1 MANE Select	c.346_348delTTTinsGTA	p.Phe116Val	missense	N/A	ENSP00000287387.2	Q96HA8-1
	NTAQ1	ENST00000523356.1	TSL:3	c.346_348delTTTinsGTA	p.Phe116Val	missense	N/A	ENSP00000428615.1	E5RHC2
	NTAQ1	ENST00000650311.1		c.166_168delTTTinsGTA	p.Phe56Val	missense	N/A	ENSP00000497747.1	A0A3B3ITD7

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr8-124448804;