rs16961645

chr15-48783032-T-G

Variant summary

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

The NM_001194998.2(CEP152):c.1322-802A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,084 control chromosomes in the GnomAD database, including 1,889 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 0.15 (1889 hom., cov: 32)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP152	NM_001194998.2	c.1322-802A>C		intron_variant		ENST00000380950.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP152	ENST00000380950.7	c.1322-802A>C		intron_variant		1	NM_001194998.2	A2
CEP152	ENST00000325747.9	c.1043-802A>C		intron_variant		1		A2
CEP152	ENST00000399334.7	c.1322-802A>C		intron_variant		1		P2
CEP152	ENST00000560322.5	c.1322-802A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22470 AN: 151966 Hom.: 1883 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.148 AC: 22471 AN: 152084 Hom.: 1889 Cov.: 32 AF XY: 0.150 AC XY: 11148 AN XY: 74344

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.132

Alfa AF: 0.128 Hom.: 211

Bravo AF: 0.153

Asia WGS AF: 0.220 AC: 764 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.19
Dann	Benign	0.55

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: rs16961645; hg19: chr15-49075229;