8-123438124-G-C

Variant names:

• chr8-123438124-G-C
• rs3765212
• NM_018024.3:c.508+790G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018024.3(NTAQ1):​c.508+790G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NTAQ1 NM_018024.3 intron
• Scores: Splicing: ADA: 0.00002399
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34
• Publications: 13 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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.508+790G>C		intron	N/A	NP_060494.1
	NTAQ1	NM_001283024.1		c.328+790G>C		intron	N/A	NP_001269953.1
	NTAQ1	NM_001283027.1		c.304+790G>C		intron	N/A	NP_001269956.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTAQ1	ENST00000287387.7	TSL:1 MANE Select	c.508+790G>C		intron	N/A	ENSP00000287387.2
	NTAQ1	ENST00000523356.1	TSL:3	c.509-10G>C		intron	N/A	ENSP00000428615.1
	NTAQ1	ENST00000650311.1		c.328+790G>C		intron	N/A	ENSP00000497747.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 547408 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 296380

African (AFR) AF: 0.00 AC: 0 AN: 15690

American (AMR) AF: 0.00 AC: 0 AN: 34222

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19914

East Asian (EAS) AF: 0.00 AC: 0 AN: 32014

South Asian (SAS) AF: 0.00 AC: 0 AN: 62330

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33126

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4052

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 315586

Other (OTH) AF: 0.00 AC: 0 AN: 30474

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	18
DANN	Benign	0.58
PhyloP100		3.3

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000024
dbscSNV1_RF	Benign	0.0080
SpliceAI score (max)		0.090		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: rs3765212; hg19: chr8-124450364;