Variant 15-48717160-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000561245.1(CEP152):n.152C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0073 in 455,410 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0075 ( 12 hom. )

Consequence

CEP152
ENST00000561245.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0240

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 -14 ACMG points.

BP4

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

BP6

Variant 15-48717160-G-T is Benign according to our data. Variant chr15-48717160-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645316.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0068 (1032/151704) while in subpopulation NFE AF= 0.00937 (637/67988). AF 95% confidence interval is 0.00877. There are 8 homozygotes in gnomad4. There are 497 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.48717160G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000561245.1 linkuse as main transcript	n.152C>A		non_coding_transcript_exon_variant	3/4	2		ENSP00000453591.1		H0YMG1

Frequencies

GnomAD3 genomes

AF:

0.00679

AC:

1030

AN:

151600

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00189

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.00887

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00562

Gnomad FIN

AF:

0.00720

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.00937

Gnomad OTH

AF:

0.0106

GnomAD3 exomes

AF:

0.00631

AC:

807

AN:

127982

Hom.:

AF XY:

0.00629

AC XY:

441

AN XY:

70088

show subpopulations

Gnomad AFR exome

AF:

0.00198

Gnomad AMR exome

AF:

0.00707

Gnomad ASJ exome

AF:

0.00247

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00550

Gnomad FIN exome

AF:

0.00613

Gnomad NFE exome

AF:

0.00875

Gnomad OTH exome

AF:

0.00827

GnomAD4 exome

AF:

0.00754

AC:

2291

AN:

303706

Hom.:

Cov.:

AF XY:

0.00731

AC XY:

1264

AN XY:

172956

show subpopulations

Gnomad4 AFR exome

AF:

0.00232

Gnomad4 AMR exome

AF:

0.00697

Gnomad4 ASJ exome

AF:

0.00278

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00551

Gnomad4 FIN exome

AF:

0.00760

Gnomad4 NFE exome

AF:

0.00939

Gnomad4 OTH exome

AF:

0.00781

GnomAD4 genome

AF:

0.00680

AC:

1032

AN:

151704

Hom.:

Cov.:

AF XY:

0.00671

AC XY:

497

AN XY:

74086

show subpopulations

Gnomad4 AFR

AF:

0.00189

Gnomad4 AMR

AF:

0.00886

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00604

Gnomad4 FIN

AF:

0.00720

Gnomad4 NFE

AF:

0.00937

Gnomad4 OTH

AF:

0.0105

Alfa

AF:

0.00564

Hom.:

Bravo

AF:

0.00646

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2023

CEP152: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.2

DANN

Benign

0.77

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