rs16961455

Variant names:

• chr15-48719626-C-T
• rs16961455
• ENST00000561245.1:n.143-2457G>A

Variant summary

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

The ENST00000561245.1(CEP152):​n.143-2457G>A variant causes a intron 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000561245.1	n.143-2457G>A		intron_variant	Intron 2 of 3	2		ENSP00000453591.1

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;