Variant 15-48767476-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_001194998.2(CEP152):c.2019-13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,613,916 control chromosomes in the GnomAD database, including 1,443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 506 hom., cov: 32)

Exomes 𝑓: 0.012 ( 937 hom. )

Consequence

CEP152
NM_001194998.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.749

Variant links:

Genes affected

CEP152 (HGNC:29298): (centrosomal protein 152) This gene encodes a protein that is thought to be involved with centrosome function. Mutations in this gene have been associated with primary microcephaly (MCPH4). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]

CEP152 links:

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=-0.77).

BP6

Variant 15-48767476-C-T is Benign according to our data. Variant chr15-48767476-C-T is described in ClinVar as [Benign]. Clinvar id is 136721.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-48767476-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP152	NM_001194998.2 link	c.2019-13G>A		intron_variant		ENST00000380950.7	NP_001181927.1	O94986-4Q3B7A2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CEP152	ENST00000380950.7 link	c.2019-13G>A	intron_variant	1	NM_001194998.2	ENSP00000370337.2	O94986-4
CEP152	ENST00000399334.7 link	c.2019-13G>A	intron_variant	1		ENSP00000382271.3	O94986-3
CEP152	ENST00000325747.9 link	c.1740-13G>A	intron_variant	1		ENSP00000321000.5	O94986-1

Frequencies

GnomAD3 genomes

AF:

0.0516

AC:

7846

AN:

152078

Hom.:

504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0528

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.0871

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.00188

Gnomad OTH

AF:

0.0435

GnomAD3 exomes

AF:

0.0331

AC:

8256

AN:

249490

Hom.:

465

AF XY:

0.0273

AC XY:

3692

AN XY:

135356

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.100

Gnomad ASJ exome

AF:

0.00695

Gnomad EAS exome

AF:

0.0869

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.00107

Gnomad NFE exome

AF:

0.00194

Gnomad OTH exome

AF:

0.0170

GnomAD4 exome

AF:

0.0117

AC:

17092

AN:

1461720

Hom.:

937

Cov.:

AF XY:

0.0107

AC XY:

7802

AN XY:

727152

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.0968

Gnomad4 ASJ exome

AF:

0.00593

Gnomad4 EAS exome

AF:

0.0963

Gnomad4 SAS exome

AF:

0.0121

Gnomad4 FIN exome

AF:

0.00135

Gnomad4 NFE exome

AF:

0.00117

Gnomad4 OTH exome

AF:

0.0187

GnomAD4 genome

AF:

0.0516

AC:

7854

AN:

152196

Hom.:

506

Cov.:

AF XY:

0.0497

AC XY:

3696

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.0529

Gnomad4 ASJ

AF:

0.00547

Gnomad4 EAS

AF:

0.0869

Gnomad4 SAS

AF:

0.0170

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.00188

Gnomad4 OTH

AF:

0.0430

Alfa

AF:

0.0126

Hom.:

120

Bravo

AF:

0.0626

Asia WGS

AF:

0.0570

AC:

201

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 17, 2013	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. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 03, 2025	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Microcephaly 9, primary, autosomal recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Seckel syndrome 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.067

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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