chr15-48780830-C-A

Variant names:

• chr15-48780830-C-A
• rs16961635
• NM_001194998.2:c.1577+366G>T

Variant summary

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

The NM_001194998.2(CEP152):​c.1577+366G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,048 control chromosomes in the GnomAD database, including 5,335 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 0.23 (5335 hom., cov: 32)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

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 (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP152	NM_001194998.2	c.1577+366G>T		intron_variant	Intron 12 of 26	ENST00000380950.7	NP_001181927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000380950.7	c.1577+366G>T		intron_variant	Intron 12 of 26	1	NM_001194998.2	ENSP00000370337.2
CEP152	ENST00000399334.7	c.1577+366G>T		intron_variant	Intron 12 of 25	1		ENSP00000382271.3
CEP152	ENST00000325747.9	c.1298+366G>T		intron_variant	Intron 11 of 24	1		ENSP00000321000.5
CEP152	ENST00000560322.5	n.1577+366G>T		intron_variant	Intron 12 of 12	1		ENSP00000453440.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34378 AN: 151930 Hom.: 5319 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0820

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.226 AC: 34420 AN: 152048 Hom.: 5335 Cov.: 32 AF XY: 0.226 AC XY: 16805 AN XY: 74326

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.0820

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.191

Alfa AF: 0.114 Hom.: 299

Bravo AF: 0.245

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.41

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: rs16961635; hg19: chr15-49073027;