Variant 16-67174030-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The XM_047434851.1(NOL3):c.162C>T(p.Ser54=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0808 in 1,549,782 control chromosomes in the GnomAD database, including 7,362 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 2192 hom., cov: 32)

Exomes 𝑓: 0.075 ( 5170 hom. )

Consequence

NOL3
XM_047434851.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.657

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 16-67174030-C-T is Benign according to our data. Variant chr16-67174030-C-T is described in ClinVar as [Benign]. Clinvar id is 3055509.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.657 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOL3	XM_047434851.1 linkuse as main transcript	c.162C>T	p.Ser54=	synonymous_variant	2/5		XP_047290807.1
NOL3	NM_001276309.3 linkuse as main transcript	c.-8-132C>T		intron_variant		ENST00000564992.2	NP_001263238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOL3	ENST00000564992.2 linkuse as main transcript	c.-8-132C>T		intron_variant		2	NM_001276309.3	ENSP00000457720	P2

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20377

AN:

152056

Hom.:

2184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0753

Gnomad ASJ

AF:

0.0302

Gnomad EAS

AF:

0.0181

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.0667

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0845

AC:

12660

AN:

149896

Hom.:

822

AF XY:

0.0829

AC XY:

6709

AN XY:

80882

show subpopulations

Gnomad AFR exome

AF:

0.304

Gnomad AMR exome

AF:

0.0700

Gnomad ASJ exome

AF:

0.0341

Gnomad EAS exome

AF:

0.0150

Gnomad SAS exome

AF:

0.111

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.0684

Gnomad OTH exome

AF:

0.0614

GnomAD4 exome

AF:

0.0750

AC:

104763

AN:

1397608

Hom.:

5170

Cov.:

AF XY:

0.0750

AC XY:

51728

AN XY:

689900

show subpopulations

Gnomad4 AFR exome

AF:

0.299

Gnomad4 AMR exome

AF:

0.0705

Gnomad4 ASJ exome

AF:

0.0348

Gnomad4 EAS exome

AF:

0.0178

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.0673

Gnomad4 OTH exome

AF:

0.0776

GnomAD4 genome

AF:

0.134

AC:

20421

AN:

152174

Hom.:

2192

Cov.:

AF XY:

0.135

AC XY:

10045

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.298

Gnomad4 AMR

AF:

0.0754

Gnomad4 ASJ

AF:

0.0302

Gnomad4 EAS

AF:

0.0182

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.0667

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.0755

Hom.:

814

Bravo

AF:

0.137

Asia WGS

AF:

0.0980

AC:

343

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

NOL3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 06, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.5

DANN

Benign

0.68

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over