rs17465874

Positions:

• chr15-48786769-G-A
• chr15-48786769-G-T

Variant summary

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

The NM_001194998.2(CEP152):​c.1173+2032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 152,190 control chromosomes in the GnomAD database, including 586 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 0.085 (586 hom., cov: 32)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP152	NM_001194998.2	c.1173+2032C>T		intron_variant		ENST00000380950.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP152	ENST00000380950.7	c.1173+2032C>T		intron_variant		1	NM_001194998.2	A2

Frequencies

GnomAD3 genomes AF: 0.0848 AC: 12901 AN: 152072 Hom.: 585 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0848 AC: 12913 AN: 152190 Hom.: 586 Cov.: 32 AF XY: 0.0860 AC XY: 6396 AN XY: 74408

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.0972

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.0857 Hom.: 317

Bravo AF: 0.0866

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.65

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: rs17465874; hg19: chr15-49078966;