Variant 15-48811047-T-C 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.-94A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,338 control chromosomes in the GnomAD database, including 1,548 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1547 hom., cov: 33)

Exomes 𝑓: 0.073 ( 1 hom. )

Consequence

CEP152
NM_001194998.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.581

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:

(HGNC:):

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=-0.85).

BP6

Variant 15-48811047-T-C is Benign according to our data. Variant chr15-48811047-T-C is described in ClinVar as [Benign]. Clinvar id is 316436.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-48811047-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP152	NM_001194998.2 linkuse as main transcript	c.-94A>G		5_prime_UTR_variant	1/27	ENST00000380950.7
LOC124903487	XR_007064626.1 linkuse as main transcript	n.227T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP152	ENST00000380950.7 linkuse as main transcript	c.-94A>G		5_prime_UTR_variant	1/27	1	NM_001194998.2	A2	O94986-4
	ENST00000560237.1 linkuse as main transcript	n.224T>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18914

AN:

152138

Hom.:

1535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.234

Gnomad ASJ

AF:

0.0694

Gnomad EAS

AF:

0.296

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.0885

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0787

Gnomad OTH

AF:

0.124

GnomAD4 exome

AF:

0.0732

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0370

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0323

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.124

AC:

18954

AN:

152256

Hom.:

1547

Cov.:

AF XY:

0.131

AC XY:

9746

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.0694

Gnomad4 EAS

AF:

0.296

Gnomad4 SAS

AF:

0.208

Gnomad4 FIN

AF:

0.0885

Gnomad4 NFE

AF:

0.0787

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.0937

Hom.:

1157

Bravo

AF:

0.138

Asia WGS

AF:

0.278

AC:

965

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Microcephaly 9, primary, autosomal recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 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. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 23, 2020

- -

Seckel syndrome 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.2

DANN

Benign

0.70

Splicing

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