8-123438124-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018024.3(NTAQ1):c.508+790G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 698,838 control chromosomes in the GnomAD database, including 49,259 homozygotes. 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: 𝑓 0.36 (10109 hom., cov: 32)
  • Exomes 𝑓: 0.37 (39150 hom.)
• Consequence: NTAQ1 NM_018024.3 intron
• Scores: Splicing: ADA: 0.00002399
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTAQ1	NM_018024.3	c.508+790G>T		intron_variant		ENST00000287387.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTAQ1	ENST00000287387.7	c.508+790G>T		intron_variant		1	NM_018024.3	P1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55099 AN: 151920 Hom.: 10104 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.368

GnomAD3 exomes AF: 0.389 AC: 49061 AN: 126140 Hom.: 9845 AF XY: 0.387 AC XY: 26788 AN XY: 69198

Gnomad AFR exome AF: 0.360

Gnomad AMR exome AF: 0.412

Gnomad ASJ exome AF: 0.387

Gnomad EAS exome AF: 0.552

Gnomad SAS exome AF: 0.404

Gnomad FIN exome AF: 0.372

Gnomad NFE exome AF: 0.342

Gnomad OTH exome AF: 0.374

GnomAD4 exome AF: 0.372 AC: 203566 AN: 546800 Hom.: 39150 Cov.: 0 AF XY: 0.374 AC XY: 110693 AN XY: 296062

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.405

Gnomad4 ASJ exome AF: 0.391

Gnomad4 EAS exome AF: 0.577

Gnomad4 SAS exome AF: 0.404

Gnomad4 FIN exome AF: 0.374

Gnomad4 NFE exome AF: 0.342

Gnomad4 OTH exome AF: 0.370

GnomAD4 genome AF: 0.363 AC: 55129 AN: 152038 Hom.: 10109 Cov.: 32 AF XY: 0.367 AC XY: 27239 AN XY: 74318

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.372

Alfa AF: 0.360 Hom.: 2264

Bravo AF: 0.366

Asia WGS AF: 0.472 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	17
Dann	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000024
dbscSNV1_RF	Benign	0.0080
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.22		Position offset: 10

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

Publications

LitVar

Other links and lift over

dbSNP: rs3765212; hg19: chr8-124450364;