Variant chr12-88084539-TA-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_025114.4(CEP290):c.4704+46delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 50434 hom., cov: 0)

Exomes 𝑓: 0.91 ( 564349 hom. )

Consequence

CEP290
NM_025114.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.814

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:

CEP290 (HGNC:):

CEP290 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-88084539-TA-T is Benign according to our data. Variant chr12-88084539-TA-T is described in ClinVar as [Benign]. Clinvar id is 261845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-88084539-TA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP290	NM_025114.4 linkuse as main transcript	c.4704+46delT		intron_variant		ENST00000552810.6	NP_079390.3	O15078Q05BJ6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP290	ENST00000552810.6 linkuse as main transcript	c.4704+46delT		intron_variant		1	NM_025114.4	ENSP00000448012.1		O15078

Frequencies

GnomAD3 genomes

AF:

0.781

AC:

118762

AN:

151998

Hom.:

50432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.411

Gnomad AMI

AF:

0.923

Gnomad AMR

AF:

0.866

Gnomad ASJ

AF:

0.895

Gnomad EAS

AF:

0.965

Gnomad SAS

AF:

0.897

Gnomad FIN

AF:

0.963

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.928

Gnomad OTH

AF:

0.821

GnomAD3 exomes

AF:

0.894

AC:

197463

AN:

220854

Hom.:

90369

AF XY:

0.901

AC XY:

108638

AN XY:

120550

show subpopulations

Gnomad AFR exome

AF:

0.395

Gnomad AMR exome

AF:

0.922

Gnomad ASJ exome

AF:

0.907

Gnomad EAS exome

AF:

0.976

Gnomad SAS exome

AF:

0.889

Gnomad FIN exome

AF:

0.962

Gnomad NFE exome

AF:

0.931

Gnomad OTH exome

AF:

0.901

GnomAD4 exome

AF:

0.913

AC:

1225707

AN:

1342950

Hom.:

564349

Cov.:

AF XY:

0.913

AC XY:

613838

AN XY:

672200

show subpopulations

Gnomad4 AFR exome

AF:

0.394

Gnomad4 AMR exome

AF:

0.916

Gnomad4 ASJ exome

AF:

0.903

Gnomad4 EAS exome

AF:

0.955

Gnomad4 SAS exome

AF:

0.892

Gnomad4 FIN exome

AF:

0.961

Gnomad4 NFE exome

AF:

0.927

Gnomad4 OTH exome

AF:

0.889

GnomAD4 genome

AF:

0.781

AC:

118778

AN:

152116

Hom.:

50434

Cov.:

AF XY:

0.787

AC XY:

58548

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.410

Gnomad4 AMR

AF:

0.866

Gnomad4 ASJ

AF:

0.895

Gnomad4 EAS

AF:

0.965

Gnomad4 SAS

AF:

0.898

Gnomad4 FIN

AF:

0.963

Gnomad4 NFE

AF:

0.928

Gnomad4 OTH

AF:

0.823

Alfa

AF:

0.859

Hom.:

10576

Bravo

AF:

0.759

Asia WGS

AF:

0.882

AC:

3064

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

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