dbSNP rs77732888: CEP152:c.691+9C>T (chr15-48796001-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_001194998.2(CEP152):c.691+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0854 in 1,611,154 control chromosomes in the GnomAD database, including 6,593 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.071 ( 472 hom., cov: 32)

Exomes 𝑓: 0.087 ( 6121 hom. )

Consequence

CEP152
NM_001194998.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 0.00900

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=-0.67).

BP6

Variant 15-48796001-G-A is Benign according to our data. Variant chr15-48796001-G-A is described in ClinVar as [Benign]. Clinvar id is 136720.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-48796001-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP152	NM_001194998.2 link	c.691+9C>T		intron_variant	Intron 6 of 26	ENST00000380950.7	NP_001181927.1	O94986-4Q3B7A2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEP152	ENST00000380950.7 link	c.691+9C>T	intron_variant	Intron 6 of 26	1	NM_001194998.2	ENSP00000370337.2	O94986-4
CEP152	ENST00000399334.7 link	c.691+9C>T	intron_variant	Intron 6 of 25	1		ENSP00000382271.3	O94986-3
CEP152	ENST00000325747.9 link	c.412+9C>T	intron_variant	Intron 5 of 24	1		ENSP00000321000.5	O94986-1
CEP152	ENST00000560322.5 link	n.691+9C>T	intron_variant	Intron 6 of 12	1		ENSP00000453440.1	A0A075B719

Frequencies

GnomAD3 genomes

AF:

0.0707

AC:

10751

AN:

152034

Hom.:

472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0342

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.0847

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0528

Gnomad FIN

AF:

0.0294

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.0994

Gnomad OTH

AF:

0.0903

GnomAD3 exomes

AF:

0.0713

AC:

17755

AN:

249162

Hom.:

809

AF XY:

0.0739

AC XY:

9998

AN XY:

135206

show subpopulations

Gnomad AFR exome

AF:

0.0337

Gnomad AMR exome

AF:

0.0585

Gnomad ASJ exome

AF:

0.0970

Gnomad EAS exome

AF:

0.000557

Gnomad SAS exome

AF:

0.0584

Gnomad FIN exome

AF:

0.0362

Gnomad NFE exome

AF:

0.0983

Gnomad OTH exome

AF:

0.0913

GnomAD4 exome

AF:

0.0870

AC:

126885

AN:

1459002

Hom.:

6121

Cov.:

AF XY:

0.0867

AC XY:

62976

AN XY:

725954

show subpopulations

Gnomad4 AFR exome

AF:

0.0317

Gnomad4 AMR exome

AF:

0.0628

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0619

Gnomad4 FIN exome

AF:

0.0394

Gnomad4 NFE exome

AF:

0.0962

Gnomad4 OTH exome

AF:

0.0876

GnomAD4 genome

AF:

0.0707

AC:

10753

AN:

152152

Hom.:

472

Cov.:

AF XY:

0.0676

AC XY:

5026

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0342

Gnomad4 AMR

AF:

0.0846

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0528

Gnomad4 FIN

AF:

0.0294

Gnomad4 NFE

AF:

0.0994

Gnomad4 OTH

AF:

0.0888

Alfa

AF:

0.0919

Hom.:

263

Bravo

AF:

0.0711

Asia WGS

AF:

0.0240

AC:

AN:

3478

EpiCase

AF:

0.107

EpiControl

AF:

0.105

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Dec 20, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 16, 2013

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Microcephaly 9, primary, autosomal recessive

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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