dbSNP rs372967874: CEP152:c.87+19_87+27delAAAAAAAAA (chr15-48805535-CTTTTTTTTT-C) – ACMG Classification: Uncertain_significance (2 pts)

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

CEP152 links:

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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;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001194998.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP152	NM_001194998.2	MANE Select	c.87+19_87+27delAAAAAAAAA		intron	N/A	NP_001181927.1	O94986-4
	CEP152	NM_014985.4		c.87+19_87+27delAAAAAAAAA		intron	N/A	NP_055800.2	O94986-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEP152	ENST00000380950.7	TSL:1 MANE Select	c.87+19_87+27delAAAAAAAAA	intron	N/A	ENSP00000370337.2	O94986-4
CEP152	ENST00000399334.7	TSL:1	c.87+19_87+27delAAAAAAAAA	intron	N/A	ENSP00000382271.3	O94986-3
CEP152	ENST00000325747.9	TSL:1	c.87+19_87+27delAAAAAAAAA	intron	N/A	ENSP00000321000.5	O94986-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000266

AC:

AN:

1128246

Hom.:

AF XY:

0.00000177

AC XY:

AN XY:

564898

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25918

American (AMR)

AF:

0.00

AC:

AN:

32310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19798

East Asian (EAS)

AF:

0.00

AC:

AN:

30708

South Asian (SAS)

AF:

0.00

AC:

AN:

68994

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33250

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4076

European-Non Finnish (NFE)

AF:

0.00000346

AC:

AN:

866960

Other (OTH)

AF:

0.00

AC:

AN:

46232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.24

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over