3-134495055-T-G

Position:

• chr3-134495055-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001353108.3(CEP63):​c.-25-241T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,274 control chromosomes in the GnomAD database, including 68,952 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.95 (68952 hom., cov: 32)
• Consequence: CEP63 NM_001353108.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.66

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 3-134495055-T-G is Benign according to our data. Variant chr3-134495055-T-G is described in ClinVar as [Benign]. Clinvar id is 1260431.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP63	NM_001353108.3	c.-25-241T>G		intron_variant		ENST00000675561.1	NP_001340037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP63	ENST00000675561.1	c.-25-241T>G		intron_variant			NM_001353108.3	ENSP00000502085	A1

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144707 AN: 152156 Hom.: 68900 Cov.: 32

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.956

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.951 AC: 144819 AN: 152274 Hom.: 68952 Cov.: 32 AF XY: 0.949 AC XY: 70653 AN XY: 74454

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.964

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.956

Alfa AF: 0.947 Hom.: 9822

Bravo AF: 0.956

Asia WGS AF: 0.891 AC: 3101 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.072
DANN	Benign	0.59

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: rs6804907; hg19: chr3-134213897;