Variant 1-223792505-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001031685.3(TP53BP2):c.2880C>G(p.Leu960Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 1,613,680 control chromosomes in the GnomAD database, including 10,977 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.17 ( 3475 hom., cov: 32)

Exomes 𝑓: 0.081 ( 7502 hom. )

Consequence

TP53BP2
NM_001031685.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.35

Variant links:

Genes affected

TP53BP2 (HGNC:12000): (tumor protein p53 binding protein 2) This gene encodes a member of the ASPP (apoptosis-stimulating protein of p53) family of p53 interacting proteins. The protein contains four ankyrin repeats and an SH3 domain involved in protein-protein interactions. It is localized to the perinuclear region of the cytoplasm, and regulates apoptosis and cell growth through interactions with other regulatory molecules including members of the p53 family. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

TP53BP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 1-223792505-G-C is Benign according to our data. Variant chr1-223792505-G-C is described in ClinVar as [Benign]. Clinvar id is 3060669.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TP53BP2	NM_001031685.3 link	c.2880C>G	p.Leu960Leu	synonymous_variant	15/18	ENST00000343537.12	NP_001026855.2	Q13625-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TP53BP2	ENST00000343537.12 link	c.2880C>G	p.Leu960Leu	synonymous_variant	15/18	1	NM_001031685.3	ENSP00000341957.7		Q13625-3

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25756

AN:

152002

Hom.:

3466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.364

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0892

Gnomad FIN

AF:

0.0378

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0714

Gnomad OTH

AF:

0.178

GnomAD3 exomes

AF:

0.120

AC:

30224

AN:

250984

Hom.:

2793

AF XY:

0.110

AC XY:

14985

AN XY:

135636

show subpopulations

Gnomad AFR exome

AF:

0.371

Gnomad AMR exome

AF:

0.204

Gnomad ASJ exome

AF:

0.109

Gnomad EAS exome

AF:

0.210

Gnomad SAS exome

AF:

0.0795

Gnomad FIN exome

AF:

0.0413

Gnomad NFE exome

AF:

0.0720

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.0811

AC:

118481

AN:

1461558

Hom.:

7502

Cov.:

AF XY:

0.0805

AC XY:

58500

AN XY:

727070

show subpopulations

Gnomad4 AFR exome

AF:

0.370

Gnomad4 AMR exome

AF:

0.201

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.211

Gnomad4 SAS exome

AF:

0.0776

Gnomad4 FIN exome

AF:

0.0414

Gnomad4 NFE exome

AF:

0.0630

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.170

AC:

25805

AN:

152122

Hom.:

3475

Cov.:

AF XY:

0.168

AC XY:

12472

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.364

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.0882

Gnomad4 FIN

AF:

0.0378

Gnomad4 NFE

AF:

0.0713

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.0918

Hom.:

692

Bravo

AF:

0.193

Asia WGS

AF:

0.158

AC:

551

AN:

3478

EpiCase

AF:

0.0798

EpiControl

AF:

0.0801

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TP53BP2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 18, 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

-0.49

CADD

Benign

5.3

DANN

Benign

0.71

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