rs10902723

chr1-26242051-T-Cchr1-26242051-T-G

Variant summary

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

The NM_001319944.2(CEP85):c.56-2115T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,198 control chromosomes in the GnomAD database, including 22,463 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 0.53 (22463 hom., cov: 31)
• Consequence: CEP85 NM_001319944.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

Genes affected

CEP85 (HGNC:25309): (centrosomal protein 85) This gene encodes a protein that belongs to the centrosome-associated family of proteins. The centrosome is a subcellular organelle in the animal cell that functions as a microtubule organizing center and is involved in cell-cycle progression. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP85	NM_001319944.2	c.56-2115T>C		intron_variant		ENST00000451429.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP85	ENST00000451429.8	c.56-2115T>C		intron_variant		2	NM_001319944.2	A1
CEP85	ENST00000252992.8	c.56-2115T>C		intron_variant		1		P4
CEP85	ENST00000640292.2	c.55+2213T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80254 AN: 151076 Hom.: 22457 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.531 AC: 80290 AN: 151198 Hom.: 22463 Cov.: 31 AF XY: 0.520 AC XY: 38442 AN XY: 73876

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.532

Alfa AF: 0.540 Hom.: 3447

Bravo AF: 0.518

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.39
Dann	Benign	0.37

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: rs10902723; hg19: chr1-26568542;