3-134558353-AT-ATT

Variant names:

• chr3-134558353-A-AT
• rs35934324
• NM_001353108.3:c.1673+12dupT

Variant summary

Our verdict is Benign. The variant received -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]

ENSG00000288700 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CEP63	NM_001353108.3	c.1673+12dupT		intron_variant	Intron 13 of 14	ENST00000675561.1	NP_001340037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP63	ENST00000675561.1	c.1673+12dupT		intron_variant	Intron 13 of 14		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

GnomAD2 exomes AF: 0.284 AC: 69824 AN: 245438 AF XY: 0.293

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 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 AC: 11422 AN: 32558

Gnomad4 AMR exome AF: 0.170 AC: 7566 AN: 44546

Gnomad4 ASJ exome AF: 0.301 AC: 7770 AN: 25850

Gnomad4 EAS exome AF: 0.192 AC: 7549 AN: 39378

Gnomad4 SAS exome AF: 0.330 AC: 28114 AN: 85260

Gnomad4 FIN exome AF: 0.265 AC: 14121 AN: 53274

Gnomad4 NFE exome AF: 0.319 AC: 342814 AN: 1075334

Gnomad4 Remaining exome AF: 0.300 AC: 17719 AN: 58980

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 AC: 0.357553 AN: 0.357553

Gnomad4 AMR AF: 0.253 AC: 0.25311 AN: 0.25311

Gnomad4 ASJ AF: 0.305 AC: 0.304724 AN: 0.304724

Gnomad4 EAS AF: 0.178 AC: 0.178254 AN: 0.178254

Gnomad4 SAS AF: 0.321 AC: 0.320539 AN: 0.320539

Gnomad4 FIN AF: 0.263 AC: 0.262765 AN: 0.262765

Gnomad4 NFE AF: 0.325 AC: 0.325442 AN: 0.325442

Gnomad4 OTH AF: 0.327 AC: 0.327488 AN: 0.327488

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

Apr 15, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=100/0	polymorphism (auto)

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;