12-88103061-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_025114.4(CEP290):​c.2818-50G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 1,280,644 control chromosomes in the GnomAD database, including 526,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 50396 hom., cov: 31)
Exomes 𝑓: 0.92 ( 476443 hom. )

Consequence

CEP290
NM_025114.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.639
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 12-88103061-C-G is Benign according to our data. Variant chr12-88103061-C-G is described in ClinVar as [Benign]. Clinvar id is 126253.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
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
CEP290NM_025114.4 linkc.2818-50G>C intron_variant ENST00000552810.6 NP_079390.3 O15078Q05BJ6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEP290ENST00000552810.6 linkc.2818-50G>C intron_variant 1 NM_025114.4 ENSP00000448012.1 O15078

Frequencies

GnomAD3 genomes
AF:
0.781
AC:
118678
AN:
151884
Hom.:
50394
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.410
Gnomad AMI
AF:
0.923
Gnomad AMR
AF:
0.866
Gnomad ASJ
AF:
0.895
Gnomad EAS
AF:
0.965
Gnomad SAS
AF:
0.898
Gnomad FIN
AF:
0.963
Gnomad MID
AF:
0.921
Gnomad NFE
AF:
0.928
Gnomad OTH
AF:
0.821
GnomAD3 exomes
AF:
0.904
AC:
68734
AN:
76008
Hom.:
31574
AF XY:
0.910
AC XY:
38022
AN XY:
41794
show subpopulations
Gnomad AFR exome
AF:
0.399
Gnomad AMR exome
AF:
0.904
Gnomad ASJ exome
AF:
0.908
Gnomad EAS exome
AF:
0.969
Gnomad SAS exome
AF:
0.887
Gnomad FIN exome
AF:
0.963
Gnomad NFE exome
AF:
0.927
Gnomad OTH exome
AF:
0.904
GnomAD4 exome
AF:
0.916
AC:
1033778
AN:
1128642
Hom.:
476443
Cov.:
14
AF XY:
0.916
AC XY:
509847
AN XY:
556586
show subpopulations
Gnomad4 AFR exome
AF:
0.410
Gnomad4 AMR exome
AF:
0.900
Gnomad4 ASJ exome
AF:
0.903
Gnomad4 EAS exome
AF:
0.948
Gnomad4 SAS exome
AF:
0.892
Gnomad4 FIN exome
AF:
0.961
Gnomad4 NFE exome
AF:
0.928
Gnomad4 OTH exome
AF:
0.891
GnomAD4 genome
AF:
0.781
AC:
118694
AN:
152002
Hom.:
50396
Cov.:
31
AF XY:
0.787
AC XY:
58488
AN XY:
74326
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:
0.899
Gnomad4 FIN
AF:
0.963
Gnomad4 NFE
AF:
0.928
Gnomad4 OTH
AF:
0.822
Alfa
AF:
0.856
Hom.:
9636
Bravo
AF:
0.759
Asia WGS
AF:
0.880
AC:
3055
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:2
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Likely benign, no assertion criteria providedclinical testingGenetic 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:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 26, 2018- -
Senior-Loken syndrome 6 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 22, 2021- -
Bardet-Biedl syndrome 14 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 22, 2021- -
Meckel syndrome, type 4 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 22, 2021- -
Joubert syndrome 5 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 22, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.2
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs2471532; hg19: chr12-88496838; API