Genetic Variant NTAQ1:c.508+790G>T (chr8-123438124-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Publications

13 publications found

Variant links:

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]

NTAQ1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NTAQ1	NM_018024.3	MANE Select	c.508+790G>T	intron	N/A	NP_060494.1	Q96HA8-1
NTAQ1	NM_001283024.1		c.328+790G>T	intron	N/A	NP_001269953.1	Q96HA8-2
NTAQ1	NM_001283027.1		c.304+790G>T	intron	N/A	NP_001269956.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NTAQ1	ENST00000287387.7	TSL:1 MANE Select	c.508+790G>T	intron	N/A	ENSP00000287387.2	Q96HA8-1
NTAQ1	ENST00000523356.1	TSL:3	c.509-10G>T	intron	N/A	ENSP00000428615.1	E5RHC2
NTAQ1	ENST00000650311.1		c.328+790G>T	intron	N/A	ENSP00000497747.1	A0A3B3ITD7

Frequencies

GnomAD3 genomes

AF:

0.363

AC:

55099

AN:

151920

Hom.:

10104

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.389

AC:

49061

AN:

126140

AF XY:

0.387

show subpopulations

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 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.:

AF XY:

0.374

AC XY:

110693

AN XY:

296062

show subpopulations

African (AFR)

AF:

0.350

AC:

5479

AN:

15672

American (AMR)

AF:

0.405

AC:

13834

AN:

34154

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

7776

AN:

19894

East Asian (EAS)

AF:

0.577

AC:

18458

AN:

31986

South Asian (SAS)

AF:

0.404

AC:

25122

AN:

62250

European-Finnish (FIN)

AF:

0.374

AC:

12363

AN:

33098

Middle Eastern (MID)

AF:

0.349

AC:

1414

AN:

4052

European-Non Finnish (NFE)

AF:

0.342

AC:

107844

AN:

315248

Other (OTH)

AF:

0.370

AC:

11276

AN:

30446

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

5816

11633

17449

23266

29082

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

662

1324

1986

2648

3310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.363

AC:

55129

AN:

152038

Hom.:

10109

Cov.:

AF XY:

0.367

AC XY:

27239

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.351

AC:

14568

AN:

41466

American (AMR)

AF:

0.398

AC:

6072

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1325

AN:

3470

East Asian (EAS)

AF:

0.561

AC:

2900

AN:

5170

South Asian (SAS)

AF:

0.414

AC:

1996

AN:

4820

European-Finnish (FIN)

AF:

0.361

AC:

3809

AN:

10556

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.344

AC:

23379

AN:

67984

Other (OTH)

AF:

0.372

AC:

785

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1803

3606

5408

7211

9014

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.359

Hom.:

2311

Bravo

AF:

0.366

Asia WGS

AF:

0.472

AC:

1639

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

3.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over