Variant 3-134507127-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001353108.3(CEP63):c.63T>C(p.Cys21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,612,436 control chromosomes in the GnomAD database, including 22,464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 1922 hom., cov: 31)

Exomes 𝑓: 0.17 ( 20542 hom. )

Consequence

CEP63
NM_001353108.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.66

Variant links:

Genes affected

CEP63 (HGNC:25815): (centrosomal protein 63) This gene encodes a protein with six coiled-coil domains. The protein is localized to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. Several alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

CEP63 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 3-134507127-T-C is Benign according to our data. Variant chr3-134507127-T-C is described in ClinVar as [Benign]. Clinvar id is 128712.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP63	NM_001353108.3 linkuse as main transcript	c.63T>C	p.Cys21=	synonymous_variant	3/15	ENST00000675561.1	NP_001340037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP63	ENST00000675561.1 linkuse as main transcript	c.63T>C	p.Cys21=	synonymous_variant	3/15		NM_001353108.3	ENSP00000502085	A1	Q96MT8-1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23833

AN:

151820

Hom.:

1919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.142

GnomAD3 exomes

AF:

0.171

AC:

42982

AN:

251218

Hom.:

3889

AF XY:

0.169

AC XY:

22999

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.126

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.217

Gnomad SAS exome

AF:

0.176

Gnomad FIN exome

AF:

0.231

Gnomad NFE exome

AF:

0.166

Gnomad OTH exome

AF:

0.153

GnomAD4 exome

AF:

0.166

AC:

241908

AN:

1460498

Hom.:

20542

Cov.:

AF XY:

0.166

AC XY:

120377

AN XY:

726608

show subpopulations

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.162

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.234

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.161

GnomAD4 genome

AF:

0.157

AC:

23840

AN:

151938

Hom.:

1922

Cov.:

AF XY:

0.159

AC XY:

11788

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.149

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.204

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.224

Gnomad4 NFE

AF:

0.165

Gnomad4 OTH

AF:

0.140

Alfa

AF:

0.159

Hom.:

3915

Bravo

AF:

0.152

Asia WGS

AF:

0.210

AC:

731

AN:

3478

EpiCase

AF:

0.158

EpiControl

AF:

0.152

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Aug 15, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

9.6

DANN

Benign

0.86

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