Genetic Variant CEP152:c.2280+1400_2280+1423dupAAAAAAAAAAAAAAAAAAAAAAAA (chr15-48765636-A-ATTTTTTTTTTTTTTTTTTTTTTTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001194998.2(CEP152):c.2280+1400_2280+1423dupAAAAAAAAAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000061 ( 1 hom., cov: 0)

Exomes 𝑓: 0.000028 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CEP152
NM_001194998.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.322

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP152	NM_001194998.2 link	c.2280+1400_2280+1423dupAAAAAAAAAAAAAAAAAAAAAAAA		intron_variant	Intron 17 of 26	ENST00000380950.7	NP_001181927.1	O94986-4Q3B7A2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEP152	ENST00000380950.7 link	c.2280+1423_2280+1424insAAAAAAAAAAAAAAAAAAAAAAAA	intron_variant	Intron 17 of 26	1	NM_001194998.2	ENSP00000370337.2	O94986-4
CEP152	ENST00000399334.7 link	c.2280+1423_2280+1424insAAAAAAAAAAAAAAAAAAAAAAAA	intron_variant	Intron 17 of 25	1		ENSP00000382271.3	O94986-3
CEP152	ENST00000325747.9 link	c.2001+1423_2001+1424insAAAAAAAAAAAAAAAAAAAAAAAA	intron_variant	Intron 16 of 24	1		ENSP00000321000.5	O94986-1

Frequencies

GnomAD3 genomes

AF:

0.0000614

AC:

AN:

48844

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000226

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000284

AC:

AN:

140612

Hom.:

Cov.:

AF XY:

0.0000470

AC XY:

AN XY:

85102

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

2400

American (AMR)

AF:

0.00

AC:

AN:

6056

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4452

East Asian (EAS)

AF:

0.00

AC:

AN:

3274

South Asian (SAS)

AF:

0.0000660

AC:

AN:

30314

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6018

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1162

European-Non Finnish (NFE)

AF:

0.0000248

AC:

AN:

80676

Other (OTH)

AF:

0.00

AC:

AN:

6260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000614

AC:

AN:

48864

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

21992

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000225

AC:

AN:

13324

American (AMR)

AF:

0.00

AC:

AN:

2790

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1430

East Asian (EAS)

AF:

0.00

AC:

AN:

1376

South Asian (SAS)

AF:

0.00

AC:

AN:

954

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1448

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

26448

Other (OTH)

AF:

0.00

AC:

AN:

670

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.375

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.32

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar for variant 15:48765636 A>ATTTTTTTTTTTTTTTTTTTTTTTT . It may be empty.

15-48765636-ATTTTTTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over