GeneBe

10-92111309-G-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014912.5(CPEB3):​c.1454-115C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000168 in 593,594 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
Exomes 𝑓: 0.0000017 ( 0 hom. )

Consequence

CPEB3
NM_014912.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

9 publications found
Variant links:
Genes affected
CPEB3 (HGNC:21746): (cytoplasmic polyadenylation element binding protein 3) Enables mRNA 3'-UTR binding activity and translation factor activity, RNA binding. Involved in cellular response to amino acid stimulus; negative regulation of transcription by RNA polymerase II; and positive regulation of mRNA catabolic process. Located in several cellular components, including cytosol; midbody; and nucleoplasm. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]
CPEB3 Gene-Disease associations (from GenCC):
  • Tourette syndrome
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CPEB3NM_014912.5 linkc.1454-115C>G intron_variant Intron 6 of 9 ENST00000265997.5 NP_055727.3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CPEB3ENST00000265997.5 linkc.1454-115C>G intron_variant Intron 6 of 9 1 NM_014912.5 ENSP00000265997.4
CPEB3ENST00000412050.8 linkc.1412-115C>G intron_variant Intron 6 of 9 1 ENSP00000398310.2
CPEB3ENST00000614585.4 linkc.1454-115C>G intron_variant Intron 6 of 9 5 ENSP00000482128.1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
0.00000168
AC:
1
AN:
593594
Hom.:
0
AF XY:
0.00000315
AC XY:
1
AN XY:
317400
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
16050
American (AMR)
AF:
0.00
AC:
0
AN:
34556
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
17608
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35536
South Asian (SAS)
AF:
0.00
AC:
0
AN:
58852
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47844
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2270
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
349660
Other (OTH)
AF:
0.0000320
AC:
1
AN:
31218
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
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.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.62
DANN
Benign
0.63
PhyloP100
-1.6

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

Other links and lift over

dbSNP: rs701846; hg19: chr10-93871066; API