Genetic Variant CEP290:c.3574-9delT (chr12-88089495-TA-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_025114.4(CEP290):c.3574-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.88 ( 59932 hom., cov: 0)

Exomes 𝑓: 0.94 ( 552196 hom. )

Consequence

CEP290
NM_025114.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: 0.208

Variant links:

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]

CEP290 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-88089495-TA-T is Benign according to our data. Variant chr12-88089495-TA-T is described in ClinVar as [Benign]. Clinvar id is 96170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-88089495-TA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP290	NM_025114.4 link	c.3574-9delT		intron_variant	Intron 30 of 53	ENST00000552810.6	NP_079390.3	O15078Q05BJ6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP290	ENST00000552810.6 link	c.3574-9delT		intron_variant	Intron 30 of 53	1	NM_025114.4	ENSP00000448012.1		O15078

Frequencies

GnomAD3 genomes

AF:

0.882

AC:

133923

AN:

151880

Hom.:

59916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.713

Gnomad AMI

AF:

0.953

Gnomad AMR

AF:

0.919

Gnomad ASJ

AF:

0.896

Gnomad EAS

AF:

0.988

Gnomad SAS

AF:

0.901

Gnomad FIN

AF:

0.988

Gnomad MID

AF:

0.934

Gnomad NFE

AF:

0.948

Gnomad OTH

AF:

0.893

GnomAD3 exomes

AF:

0.931

AC:

76331

AN:

82002

Hom.:

35734

AF XY:

0.932

AC XY:

40011

AN XY:

42938

show subpopulations

Gnomad AFR exome

AF:

0.705

Gnomad AMR exome

AF:

0.939

Gnomad ASJ exome

AF:

0.913

Gnomad EAS exome

AF:

0.990

Gnomad SAS exome

AF:

0.894

Gnomad FIN exome

AF:

0.987

Gnomad NFE exome

AF:

0.950

Gnomad OTH exome

AF:

0.929

GnomAD4 exome

AF:

0.942

AC:

1170044

AN:

1242604

Hom.:

552196

Cov.:

AF XY:

0.941

AC XY:

565434

AN XY:

600924

show subpopulations

Gnomad4 AFR exome

AF:

0.708

Gnomad4 AMR exome

AF:

0.939

Gnomad4 ASJ exome

AF:

0.906

Gnomad4 EAS exome

AF:

0.993

Gnomad4 SAS exome

AF:

0.898

Gnomad4 FIN exome

AF:

0.984

Gnomad4 NFE exome

AF:

0.949

Gnomad4 OTH exome

AF:

0.925

GnomAD4 genome

AF:

0.881

AC:

133981

AN:

151998

Hom.:

59932

Cov.:

AF XY:

0.885

AC XY:

65778

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.712

Gnomad4 AMR

AF:

0.919

Gnomad4 ASJ

AF:

0.896

Gnomad4 EAS

AF:

0.988

Gnomad4 SAS

AF:

0.902

Gnomad4 FIN

AF:

0.988

Gnomad4 NFE

AF:

0.947

Gnomad4 OTH

AF:

0.894

Alfa

AF:

0.914

Hom.:

3709

Bravo

AF:

0.869

ClinVar

Significance: Benign

Submissions summary: Benign:14

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Nov 20, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Leber congenital amaurosis

Benign:2

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 16, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Senior-Loken syndrome 6

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Jun 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Bardet-Biedl syndrome 14

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis;C0687120:Nephronophthisis

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Meckel-Gruber syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Meckel syndrome, type 4

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Renal dysplasia and retinal aplasia

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial aplasia of the vermis

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Bardet-Biedl syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joubert syndrome 5

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over