rs16961455

chr15-48719626-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561245.1(CEP152):c.143-2457G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 152,142 control chromosomes in the GnomAD database, including 549 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.069 (549 hom., cov: 32)
• Consequence: CEP152 ENST00000561245.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP152	ENST00000561245.1	c.143-2457G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10529 AN: 152024 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.0727

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0692 AC: 10523 AN: 152142 Hom.: 549 Cov.: 32 AF XY: 0.0712 AC XY: 5296 AN XY: 74378

Gnomad4 AFR AF: 0.0170

Gnomad4 AMR AF: 0.0587

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0740 Hom.: 178

Bravo AF: 0.0664

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.2
Dann	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16961455; hg19: chr15-49011823;