Variant 1-3826827-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014704.4(CEP104):c.2152-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,394,684 control chromosomes in the GnomAD database, including 77,451 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 7251 hom., cov: 33)

Exomes 𝑓: 0.33 ( 70200 hom. )

Consequence

CEP104
NM_014704.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.670

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-3826827-C-T is Benign according to our data. Variant chr1-3826827-C-T is described in ClinVar as [Benign]. Clinvar id is 1242626.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP104	NM_014704.4 linkuse as main transcript	c.2152-83G>A		intron_variant		ENST00000378230.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP104	ENST00000378230.8 linkuse as main transcript	c.2152-83G>A		intron_variant		5	NM_014704.4	P4	O60308-1

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44620

AN:

151584

Hom.:

7244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.508

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.332

AC:

412118

AN:

1242982

Hom.:

70200

AF XY:

0.336

AC XY:

210865

AN XY:

627878

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.343

Gnomad4 ASJ exome

AF:

0.320

Gnomad4 EAS exome

AF:

0.449

Gnomad4 SAS exome

AF:

0.446

Gnomad4 FIN exome

AF:

0.410

Gnomad4 NFE exome

AF:

0.317

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.294

AC:

44644

AN:

151702

Hom.:

7251

Cov.:

AF XY:

0.303

AC XY:

22419

AN XY:

74102

show subpopulations

Gnomad4 AFR

AF:

0.172

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.507

Gnomad4 SAS

AF:

0.468

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.232

Hom.:

911

Bravo

AF:

0.279

Asia WGS

AF:

0.462

AC:

1602

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.41

DANN

Benign

0.71

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.

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