15-48805535-CT-C

Position:

• chr15-48805535-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001194998.2(CEP152):​c.87+27del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 1,138,270 control chromosomes in the GnomAD database, including 31 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.015 (20 hom., cov: 26)
  • Exomes 𝑓: 0.079 (11 hom.)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.181

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-48805535-CT-C is Benign according to our data. Variant chr15-48805535-CT-C is described in ClinVar as [Benign]. Clinvar id is 1230136.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-48805535-CT-C is described in Lovd as [Likely_benign].
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP152	NM_001194998.2	c.87+27del		intron_variant		ENST00000380950.7	NP_001181927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000380950.7	c.87+27del		intron_variant		1	NM_001194998.2	ENSP00000370337	A2

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 1621 AN: 111436 Hom.: 20 Cov.: 26

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00444

Gnomad ASJ AF: 0.00272

Gnomad EAS AF: 0.000238

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.00444

Gnomad MID AF: 0.00435

Gnomad NFE AF: 0.00230

Gnomad OTH AF: 0.00683

GnomAD3 exomes AF: 0.128 AC: 12549 AN: 98152 Hom.: 14 AF XY: 0.129 AC XY: 6953 AN XY: 53738

Gnomad AFR exome AF: 0.180

Gnomad AMR exome AF: 0.0868

Gnomad ASJ exome AF: 0.0968

Gnomad EAS exome AF: 0.0522

Gnomad SAS exome AF: 0.107

Gnomad FIN exome AF: 0.178

Gnomad NFE exome AF: 0.149

Gnomad OTH exome AF: 0.127

GnomAD4 exome AF: 0.0785 AC: 80651 AN: 1026820 Hom.: 11 Cov.: 24 AF XY: 0.0787 AC XY: 40387 AN XY: 512950

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.0574

Gnomad4 ASJ exome AF: 0.0761

Gnomad4 EAS exome AF: 0.0399

Gnomad4 SAS exome AF: 0.0673

Gnomad4 FIN exome AF: 0.0991

Gnomad4 NFE exome AF: 0.0797

Gnomad4 OTH exome AF: 0.0801

GnomAD4 genome AF: 0.0146 AC: 1622 AN: 111450 Hom.: 20 Cov.: 26 AF XY: 0.0141 AC XY: 763 AN XY: 54110

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.00444

Gnomad4 ASJ AF: 0.00272

Gnomad4 EAS AF: 0.000239

Gnomad4 SAS AF: 0.000833

Gnomad4 FIN AF: 0.00444

Gnomad4 NFE AF: 0.00230

Gnomad4 OTH AF: 0.00678

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs372967874; hg19: chr15-49097732;