3-134506843-G-A

Position:

• chr3-134506843-G-A

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.45-266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 149,044 control chromosomes in the GnomAD database, including 32,908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.66 (32908 hom., cov: 24)
• Consequence: CEP63 NM_001353108.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.45

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=-1.03).
• BP6: Variant 3-134506843-G-A is Benign according to our data. Variant chr3-134506843-G-A is described in ClinVar as [Benign]. Clinvar id is 1274368.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP63	NM_001353108.3	c.45-266G>A		intron_variant		ENST00000675561.1	NP_001340037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP63	ENST00000675561.1	c.45-266G>A		intron_variant			NM_001353108.3	ENSP00000502085	A1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 98610 AN: 148942 Hom.: 32901 Cov.: 24

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.662 AC: 98654 AN: 149044 Hom.: 32908 Cov.: 24 AF XY: 0.668 AC XY: 48461 AN XY: 72544

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.662

Alfa AF: 0.666 Hom.: 4246

Bravo AF: 0.660

Asia WGS AF: 0.705 AC: 2451 AN: 3474

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	-1.0
CADD	Benign	0.11
DANN	Benign	0.55

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: rs4974478; hg19: chr3-134225685;