rs45477492

chr12-88053784-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_025114.4(CEP290):c.7035-38C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.023 in 1,055,992 control chromosomes in the GnomAD database, including 449 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.036 (151 hom., cov: 32)
  • Exomes 𝑓: 0.021 (298 hom.)
• Consequence: CEP290 NM_025114.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.172

Genes affected

CEP290 (HGNC:29021): (centrosomal protein 290) This gene encodes a protein with 13 putative coiled-coil domains, a region with homology to SMC chromosome segregation ATPases, six KID motifs, three tropomyosin homology domains and an ATP/GTP binding site motif A. The protein is localized to the centrosome and cilia and has sites for N-glycosylation, tyrosine sulfation, phosphorylation, N-myristoylation, and amidation. Mutations in this gene have been associated with Joubert syndrome and nephronophthisis and the presence of antibodies against this protein is associated with several forms of cancer. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 12-88053784-G-C is Benign according to our data. Variant chr12-88053784-G-C is described in ClinVar as [Benign]. Clinvar id is 126267.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-88053784-G-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.075 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP290	NM_025114.4	c.7035-38C>G		intron_variant		ENST00000552810.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP290	ENST00000552810.6	c.7035-38C>G		intron_variant		1	NM_025114.4	P4

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5413 AN: 152092 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0340

GnomAD3 exomes AF: 0.0197 AC: 2542 AN: 128932 Hom.: 49 AF XY: 0.0181 AC XY: 1234 AN XY: 68132

Gnomad AFR exome AF: 0.0781

Gnomad AMR exome AF: 0.0193

Gnomad ASJ exome AF: 0.00121

Gnomad EAS exome AF: 0.0138

Gnomad SAS exome AF: 0.00307

Gnomad FIN exome AF: 0.0254

Gnomad NFE exome AF: 0.0192

Gnomad OTH exome AF: 0.0191

GnomAD4 exome AF: 0.0208 AC: 18813 AN: 903782 Hom.: 298 Cov.: 12 AF XY: 0.0200 AC XY: 9202 AN XY: 460596

Gnomad4 AFR exome AF: 0.0796

Gnomad4 AMR exome AF: 0.0196

Gnomad4 ASJ exome AF: 0.00122

Gnomad4 EAS exome AF: 0.0401

Gnomad4 SAS exome AF: 0.00363

Gnomad4 FIN exome AF: 0.0235

Gnomad4 NFE exome AF: 0.0201

Gnomad4 OTH exome AF: 0.0207

GnomAD4 genome AF: 0.0357 AC: 5429 AN: 152210 Hom.: 151 Cov.: 32 AF XY: 0.0354 AC XY: 2635 AN XY: 74418

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.0274

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0235 Hom.: 15

Bravo AF: 0.0360

Asia WGS AF: 0.0180 AC: 63 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 16, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.91
Dann	Benign	0.57

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: rs45477492; hg19: chr12-88447561;