Variant 1-3815395-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014704.4(CEP104):c.*7G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 1,596,024 control chromosomes in the GnomAD database, including 5,912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.061 ( 406 hom., cov: 34)

Exomes 𝑓: 0.083 ( 5506 hom. )

Consequence

CEP104
NM_014704.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.981

Variant links:

Genes affected

CEP104 (HGNC:24866): (centrosomal protein 104) This gene encodes a centrosomal protein required for ciliogenesis and for ciliary tip structural integrity. The mammalian protein contains three amino-terminal hydrophobic domains, two glycosylation sites, four cysteine-rich motifs, and two regions with homology to the glutamate receptor ionotropic, NMDA 1 protein. During ciliogenesis, the encoded protein translocates from the distal tips of the centrioles to the tip of the elongating cilium. Knockdown of the protein in human retinal pigment cells results in severe defects in ciliogenesis with structural deformities at the ciliary tips. Allelic variants of this gene are associated with the autosomal-recessive disorder Joubert syndrome, which is characterized by a distinctive mid-hindbrain and cerebellar malformation, oculomotor apraxia, irregular breathing, developmental delay, and ataxia. [provided by RefSeq, Feb 2016]

CEP104 links:

CEP104 (HGNC:):

CEP104 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 1-3815395-C-T is Benign according to our data. Variant chr1-3815395-C-T is described in ClinVar as [Benign]. Clinvar id is 1263430.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.089 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP104	NM_014704.4 linkuse as main transcript	c.*7G>A		3_prime_UTR_variant	22/22	ENST00000378230.8	NP_055519.1	O60308-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP104	ENST00000378230 linkuse as main transcript	c.*7G>A		3_prime_UTR_variant	22/22	5	NM_014704.4	ENSP00000367476.3		O60308-1

Frequencies

GnomAD3 genomes

AF:

0.0612

AC:

9321

AN:

152212

Hom.:

406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0168

Gnomad AMI

AF:

0.0802

Gnomad AMR

AF:

0.0567

Gnomad ASJ

AF:

0.0829

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.0345

Gnomad FIN

AF:

0.0827

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0910

Gnomad OTH

AF:

0.0655

GnomAD3 exomes

AF:

0.0651

AC:

15338

AN:

235484

Hom.:

600

AF XY:

0.0669

AC XY:

8535

AN XY:

127576

show subpopulations

Gnomad AFR exome

AF:

0.0153

Gnomad AMR exome

AF:

0.0400

Gnomad ASJ exome

AF:

0.0857

Gnomad EAS exome

AF:

0.00191

Gnomad SAS exome

AF:

0.0432

Gnomad FIN exome

AF:

0.0799

Gnomad NFE exome

AF:

0.0914

Gnomad OTH exome

AF:

0.0762

GnomAD4 exome

AF:

0.0835

AC:

120531

AN:

1443694

Hom.:

5506

Cov.:

AF XY:

0.0825

AC XY:

59262

AN XY:

718214

show subpopulations

Gnomad4 AFR exome

AF:

0.0141

Gnomad4 AMR exome

AF:

0.0420

Gnomad4 ASJ exome

AF:

0.0885

Gnomad4 EAS exome

AF:

0.00821

Gnomad4 SAS exome

AF:

0.0450

Gnomad4 FIN exome

AF:

0.0780

Gnomad4 NFE exome

AF:

0.0936

Gnomad4 OTH exome

AF:

0.0758

GnomAD4 genome

AF:

0.0612

AC:

9320

AN:

152330

Hom.:

406

Cov.:

AF XY:

0.0600

AC XY:

4466

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0167

Gnomad4 AMR

AF:

0.0566

Gnomad4 ASJ

AF:

0.0829

Gnomad4 EAS

AF:

0.00386

Gnomad4 SAS

AF:

0.0350

Gnomad4 FIN

AF:

0.0827

Gnomad4 NFE

AF:

0.0909

Gnomad4 OTH

AF:

0.0643

Alfa

AF:

0.0624

Hom.:

157

Bravo

AF:

0.0594

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 03, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.36

DANN

Benign

0.69

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