GeneBe

15-48805535-CTTTTTTTTT-C

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001194998.2(CEP152):​c.87+19_87+27delAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000266 in 1,128,246 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

CEP152
NM_001194998.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236

Publications

0 publications found
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]
CEP152 Gene-Disease associations (from GenCC):
  • microcephaly with or without short stature
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • Seckel syndrome 5
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
  • microcephaly 9, primary, autosomal recessive
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • autosomal recessive primary microcephaly
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • Seckel syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEP152NM_001194998.2 linkc.87+19_87+27delAAAAAAAAA intron_variant Intron 2 of 26 ENST00000380950.7 NP_001181927.1 O94986-4Q3B7A2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEP152ENST00000380950.7 linkc.87+19_87+27delAAAAAAAAA intron_variant Intron 2 of 26 1 NM_001194998.2 ENSP00000370337.2 O94986-4

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000266
AC:
3
AN:
1128246
Hom.:
0
AF XY:
0.00000177
AC XY:
1
AN XY:
564898
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
25918
American (AMR)
AF:
0.00
AC:
0
AN:
32310
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19798
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30708
South Asian (SAS)
AF:
0.00
AC:
0
AN:
68994
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
33250
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4076
European-Non Finnish (NFE)
AF:
0.00000346
AC:
3
AN:
866960
Other (OTH)
AF:
0.00
AC:
0
AN:
46232
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs372967874; hg19: chr15-49097732; API