Genetic Variant NM_017948.6:c.203-38A>G (chr9-92321784-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_017948.6(NOL8):c.203-38A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 990,684 control chromosomes in the GnomAD database, including 1,428 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 0.061 ( 405 hom., cov: 33)

Exomes 𝑓: 0.044 ( 1023 hom. )

Consequence

NOL8
NM_017948.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.322

Publications

6 publications found

Variant links:

Genes affected

NOL8 (HGNC:23387): (nucleolar protein 8) NOL8 binds Ras-related GTP-binding proteins (see MIM 608267) and plays a role in cell growth (Sekiguchi et al., 2004 [PubMed 14660641]).[supplied by OMIM, Mar 2008]

NOL8 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017948.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NOL8	NM_017948.6	MANE Select	c.203-38A>G	intron	N/A	NP_060418.4
NOL8	NM_001438180.1		c.203-38A>G	intron	N/A	NP_001425109.1
NOL8	NM_001438181.1		c.203-38A>G	intron	N/A	NP_001425110.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NOL8	ENST00000442668.7	TSL:1 MANE Select	c.203-38A>G	intron	N/A	ENSP00000401177.2
NOL8	ENST00000358855.8	TSL:1	c.-2-38A>G	intron	N/A	ENSP00000351723.4
NOL8	ENST00000542053.5	TSL:5	c.-2-38A>G	intron	N/A	ENSP00000440709.1

Frequencies

GnomAD3 genomes

AF:

0.0612

AC:

9316

AN:

152202

Hom.:

406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.0399

Gnomad ASJ

AF:

0.0599

Gnomad EAS

AF:

0.0396

Gnomad SAS

AF:

0.0788

Gnomad FIN

AF:

0.0187

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0417

Gnomad OTH

AF:

0.0521

GnomAD2 exomes

AF:

0.0471

AC:

4478

AN:

95128

AF XY:

0.0474

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.0321

Gnomad ASJ exome

AF:

0.0627

Gnomad EAS exome

AF:

0.0489

Gnomad FIN exome

AF:

0.0188

Gnomad NFE exome

AF:

0.0418

Gnomad OTH exome

AF:

0.0402

GnomAD4 exome

AF:

0.0439

AC:

36797

AN:

838364

Hom.:

1023

Cov.:

AF XY:

0.0449

AC XY:

19344

AN XY:

431062

show subpopulations

African (AFR)

AF:

0.118

AC:

2105

AN:

17838

American (AMR)

AF:

0.0340

AC:

538

AN:

15818

Ashkenazi Jewish (ASJ)

AF:

0.0639

AC:

1225

AN:

19178

East Asian (EAS)

AF:

0.0488

AC:

1489

AN:

30488

South Asian (SAS)

AF:

0.0696

AC:

3949

AN:

56724

European-Finnish (FIN)

AF:

0.0203

AC:

929

AN:

45662

Middle Eastern (MID)

AF:

0.0309

AC:

137

AN:

4428

European-Non Finnish (NFE)

AF:

0.0404

AC:

24616

AN:

609998

Other (OTH)

AF:

0.0473

AC:

1809

AN:

38230

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1667

3334

5002

6669

8336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.0612

AC:

9327

AN:

152320

Hom.:

405

Cov.:

AF XY:

0.0593

AC XY:

4414

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.113

AC:

4683

AN:

41558

American (AMR)

AF:

0.0399

AC:

610

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0599

AC:

208

AN:

3470

East Asian (EAS)

AF:

0.0397

AC:

206

AN:

5188

South Asian (SAS)

AF:

0.0795

AC:

384

AN:

4828

European-Finnish (FIN)

AF:

0.0187

AC:

199

AN:

10618

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0417

AC:

2835

AN:

68034

Other (OTH)

AF:

0.0535

AC:

113

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

455

910

1365

1820

2275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0517

Hom.:

Bravo

AF:

0.0645

Asia WGS

AF:

0.0900

AC:

314

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

7.6

(source)

DANN

Benign

0.62

PhyloP100

-0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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