15-48805535-CTTTTTTT-CTTTTTTTT

Variant summary

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

The NM_001194998.2(CEP152):c.87+27_87+28insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,198,422 control chromosomes in the GnomAD database, including 2,446 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (2291 hom., cov: 26)
  • Exomes 𝑓: 0.13 (155 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-C-CT is Benign according to our data. Variant chr15-48805535-C-CT is described in ClinVar as [Benign]. Clinvar id is 1278089.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP152	NM_001194998.2	c.87+27_87+28insA		intron_variant		ENST00000380950.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP152	ENST00000380950.7	c.87+27_87+28insA		intron_variant		1	NM_001194998.2	A2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 22454 AN: 111376 Hom.: 2287 Cov.: 26

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0595

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.208

GnomAD3 exomes AF: 0.164 AC: 16145 AN: 98152 Hom.: 69 AF XY: 0.160 AC XY: 8593 AN XY: 53738

Gnomad AFR exome AF: 0.143

Gnomad AMR exome AF: 0.267

Gnomad ASJ exome AF: 0.0908

Gnomad EAS exome AF: 0.331

Gnomad SAS exome AF: 0.192

Gnomad FIN exome AF: 0.139

Gnomad NFE exome AF: 0.110

Gnomad OTH exome AF: 0.141

GnomAD4 exome AF: 0.133 AC: 144730 AN: 1087034 Hom.: 155 Cov.: 24 AF XY: 0.132 AC XY: 71997 AN XY: 543514

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.186

Gnomad4 ASJ exome AF: 0.0861

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.177

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.123

Gnomad4 OTH exome AF: 0.137

GnomAD4 genome AF: 0.202 AC: 22461 AN: 111388 Hom.: 2291 Cov.: 26 AF XY: 0.213 AC XY: 11508 AN XY: 54072

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.214

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 10, 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;