dbSNP rs8057598: NOL3:c.*298A>G (chr16-67175352-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001276309.3(NOL3):c.*298A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,293,680 control chromosomes in the GnomAD database, including 16,053 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 0.22 ( 7602 hom., cov: 33)

Exomes 𝑓: 0.085 ( 8451 hom. )

Consequence

NOL3
NM_001276309.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.169

Publications

18 publications found

Variant links:

Genes affected

NOL3 (HGNC:7869): (nucleolar protein 3) This gene encodes an anti-apoptotic protein that has been shown to down-regulate the enzyme activities of caspase 2, caspase 8 and tumor protein p53. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

NOL3 links:

MATCAP1 (HGNC:34408): (microtubule associated tyrosine carboxypeptidase 1)

MATCAP1 links:

Genome browser will be placed here

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOL3	NM_001276309.3 link	c.*298A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000564992.2	NP_001263238.1
MATCAP1	NM_001040715.2 link	c.*1459T>C		downstream_gene_variant		ENST00000563902.2	NP_001035805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL3	ENST00000564992.2 link	c.*298A>G		3_prime_UTR_variant	Exon 4 of 4	2	NM_001276309.3	ENSP00000457720.2
MATCAP1	ENST00000563902.2 link	c.*1459T>C		downstream_gene_variant		1	NM_001040715.2	ENSP00000456838.1

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33481

AN:

152002

Hom.:

7567

Cov.:

show subpopulations

Gnomad AFR

AF:

0.585

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.0216

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0691

Gnomad OTH

AF:

0.163

GnomAD4 exome

AF:

0.0851

AC:

97157

AN:

1141560

Hom.:

8451

Cov.:

AF XY:

0.0851

AC XY:

46284

AN XY:

544184

show subpopulations

African (AFR)

AF:

0.616

AC:

15586

AN:

25282

American (AMR)

AF:

0.102

AC:

1191

AN:

11650

Ashkenazi Jewish (ASJ)

AF:

0.0398

AC:

620

AN:

15580

East Asian (EAS)

AF:

0.0194

AC:

554

AN:

28496

South Asian (SAS)

AF:

0.173

AC:

6259

AN:

36270

European-Finnish (FIN)

AF:

0.111

AC:

2443

AN:

21978

Middle Eastern (MID)

AF:

0.0945

AC:

291

AN:

3078

European-Non Finnish (NFE)

AF:

0.0686

AC:

65413

AN:

953076

Other (OTH)

AF:

0.104

AC:

4800

AN:

46150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

3522

7044

10567

14089

17611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2934

5868

8802

11736

14670

<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:

0.221

AC:

33576

AN:

152120

Hom.:

7602

Cov.:

AF XY:

0.219

AC XY:

16317

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.585

AC:

24272

AN:

41458

American (AMR)

AF:

0.116

AC:

1770

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0343

AC:

119

AN:

3472

East Asian (EAS)

AF:

0.0216

AC:

112

AN:

5178

South Asian (SAS)

AF:

0.169

AC:

816

AN:

4830

European-Finnish (FIN)

AF:

0.124

AC:

1310

AN:

10600

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0691

AC:

4696

AN:

67966

Other (OTH)

AF:

0.163

AC:

344

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

960

1920

2881

3841

4801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.123

Hom.:

3289

Bravo

AF:

0.233

Asia WGS

AF:

0.151

AC:

525

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.7

(source)

DANN

Benign

0.66

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over