3-134514250-A-G

Position:

• chr3-134514250-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001353108.3(CEP63):​c.222+6964A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,068 control chromosomes in the GnomAD database, including 31,257 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (31257 hom., cov: 32)
• Consequence: CEP63 NM_001353108.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP63	NM_001353108.3	c.222+6964A>G		intron_variant		ENST00000675561.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP63	ENST00000675561.1	c.222+6964A>G		intron_variant			NM_001353108.3	A1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96337 AN: 151950 Hom.: 31255 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.634 AC: 96362 AN: 152068 Hom.: 31257 Cov.: 32 AF XY: 0.641 AC XY: 47620 AN XY: 74334

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.636

Alfa AF: 0.675 Hom.: 50651

Bravo AF: 0.630

Asia WGS AF: 0.693 AC: 2406 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	11
DANN	Benign	0.65

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: rs10935120; hg19: chr3-134233092;