rs784416

chr15-48720728-G-C

Variant summary

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

The ENST00000561245.1(CEP152):c.143-3559C>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 152,220 control chromosomes in the GnomAD database, including 71,998 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 0.97 (71998 hom., cov: 30)
• Consequence: CEP152 ENST00000561245.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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.143-3559C>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.971 AC: 147660 AN: 152100 Hom.: 71947 Cov.: 30

Gnomad AFR AF: 0.991

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.971 AC: 147761 AN: 152220 Hom.: 71998 Cov.: 30 AF XY: 0.966 AC XY: 71893 AN XY: 74426

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.958

Alfa AF: 0.985 Hom.: 8116

Bravo AF: 0.962

Asia WGS AF: 0.827 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.1
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784416; hg19: chr15-49012925;