rs7174453

Positions:

• chr15-48725156-A-G

Variant summary

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

The ENST00000561245.1(CEP152):​c.143-7987T>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,218 control chromosomes in the GnomAD database, including 391 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 0.046 (391 hom., cov: 32)
• Consequence: CEP152 ENST00000561245.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000561245.1	c.143-7987T>C		intron_variant, NMD_transcript_variant		2		ENSP00000453591

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7044 AN: 152100 Hom.: 389 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00185

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0463 AC: 7054 AN: 152218 Hom.: 391 Cov.: 32 AF XY: 0.0449 AC XY: 3338 AN XY: 74424

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0516

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.0880

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.00185

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0226 Hom.: 33

Bravo AF: 0.0563

Asia WGS AF: 0.0570 AC: 198 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0080
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7174453; hg19: chr15-49017353;