rs2289179

chr15-48782342-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001194998.2(CEP152):c.1322-112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 860,446 control chromosomes in the GnomAD database, including 17,355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (5733 hom., cov: 32)
  • Exomes 𝑓: 0.16 (11622 hom.)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.524

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 15-48782342-C-T is Benign according to our data. Variant chr15-48782342-C-T is described in ClinVar as [Benign]. Clinvar id is 1249557.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP152	NM_001194998.2	c.1322-112G>A		intron_variant		ENST00000380950.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP152	ENST00000380950.7	c.1322-112G>A		intron_variant		1	NM_001194998.2	A2
CEP152	ENST00000325747.9	c.1043-112G>A		intron_variant		1		A2
CEP152	ENST00000399334.7	c.1322-112G>A		intron_variant		1		P2
CEP152	ENST00000560322.5	c.1322-112G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35332 AN: 151954 Hom.: 5718 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.195

GnomAD4 exome AF: 0.158 AC: 111688 AN: 708374 Hom.: 11622 AF XY: 0.154 AC XY: 57929 AN XY: 375710

Gnomad4 AFR exome AF: 0.453

Gnomad4 AMR exome AF: 0.229

Gnomad4 ASJ exome AF: 0.0796

Gnomad4 EAS exome AF: 0.444

Gnomad4 SAS exome AF: 0.134

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.128

Gnomad4 OTH exome AF: 0.168

GnomAD4 genome AF: 0.233 AC: 35373 AN: 152072 Hom.: 5733 Cov.: 32 AF XY: 0.232 AC XY: 17252 AN XY: 74360

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0819

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.193

Alfa AF: 0.181 Hom.: 614

Bravo AF: 0.252

Asia WGS AF: 0.290 AC: 1010 AN: 3478

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

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.59
Dann	Benign	0.30

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: rs2289179; hg19: chr15-49074539; COSMIC: COSV57857211; COSMIC: COSV57857211;