3-134558353-AT-ATT

Position:

• chr3-134558353-AT-ATT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001353108.3(CEP63):​c.1673+12dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,572,726 control chromosomes in the GnomAD database, including 78,246 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (7984 hom., cov: 0)
  • Exomes 𝑓: 0.31 (70262 hom.)
• Consequence: CEP63 NM_001353108.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 1.34

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-134558353-A-AT is Benign according to our data. Variant chr3-134558353-A-AT is described in ClinVar as [Benign]. Clinvar id is 210701.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP63	NM_001353108.3	c.1673+12dupT		intron_variant		ENST00000675561.1	NP_001340037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP63	ENST00000675561.1	c.1673+12dupT		intron_variant			NM_001353108.3	ENSP00000502085.1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48331 AN: 151906 Hom.: 7983 Cov.: 0

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.328

GnomAD3 exomes AF: 0.284 AC: 69824 AN: 245438 Hom.: 10538 AF XY: 0.293 AC XY: 39039 AN XY: 133412

Gnomad AFR exome AF: 0.354

Gnomad AMR exome AF: 0.161

Gnomad ASJ exome AF: 0.305

Gnomad EAS exome AF: 0.169

Gnomad SAS exome AF: 0.337

Gnomad FIN exome AF: 0.258

Gnomad NFE exome AF: 0.320

Gnomad OTH exome AF: 0.294

GnomAD4 exome AF: 0.309 AC: 438710 AN: 1420702 Hom.: 70262 Cov.: 26 AF XY: 0.311 AC XY: 220556 AN XY: 709472

Gnomad4 AFR exome AF: 0.351

Gnomad4 AMR exome AF: 0.170

Gnomad4 ASJ exome AF: 0.301

Gnomad4 EAS exome AF: 0.192

Gnomad4 SAS exome AF: 0.330

Gnomad4 FIN exome AF: 0.265

Gnomad4 NFE exome AF: 0.319

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.318 AC: 48358 AN: 152024 Hom.: 7984 Cov.: 0 AF XY: 0.312 AC XY: 23168 AN XY: 74294

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.327

Alfa AF: 0.312 Hom.: 1198

Asia WGS AF: 0.242 AC: 841 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

Apr 15, 2013

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35934324; hg19: chr3-134277195;