15-48764473-T-G

Variant names:

• chr15-48764473-T-G
• rs8041414
• NM_001194998.2:c.2281-1801A>C

Variant summary

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

The NM_001194998.2(CEP152):​c.2281-1801A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,054 control chromosomes in the GnomAD database, including 12,028 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 0.34 (12028 hom., cov: 32)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP152	NM_001194998.2	c.2281-1801A>C		intron_variant	Intron 17 of 26	ENST00000380950.7	NP_001181927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000380950.7	c.2281-1801A>C		intron_variant	Intron 17 of 26	1	NM_001194998.2	ENSP00000370337.2
CEP152	ENST00000399334.7	c.2281-1801A>C		intron_variant	Intron 17 of 25	1		ENSP00000382271.3
CEP152	ENST00000325747.9	c.2002-1801A>C		intron_variant	Intron 16 of 24	1		ENSP00000321000.5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50896 AN: 151936 Hom.: 11992 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.335 AC: 50972 AN: 152054 Hom.: 12028 Cov.: 32 AF XY: 0.337 AC XY: 25033 AN XY: 74350

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.293

Alfa AF: 0.222 Hom.: 1124

Bravo AF: 0.370

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.094
DANN	Benign	0.39

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: rs8041414; hg19: chr15-49056670; COSMIC: COSV57857444; COSMIC: COSV57857444;