rs58156069

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000380950.7(CEP152):​c.833-4G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

CEP152
ENST00000380950.7 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00002383
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.136
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CEP152NM_001194998.2 linkuse as main transcriptc.833-4G>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000380950.7 NP_001181927.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEP152ENST00000380950.7 linkuse as main transcriptc.833-4G>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_001194998.2 ENSP00000370337 A2O94986-4
CEP152ENST00000325747.9 linkuse as main transcriptc.554-4G>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 ENSP00000321000 A2O94986-1
CEP152ENST00000399334.7 linkuse as main transcriptc.833-4G>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 ENSP00000382271 P2O94986-3
CEP152ENST00000560322.5 linkuse as main transcriptc.833-4G>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 ENSP00000453440

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
6.8
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000024
dbscSNV1_RF
Benign
0.0080
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-49083577; API