rs701846

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000265997.5(CPEB3):​c.1454-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 744,904 control chromosomes in the GnomAD database, including 141,741 homozygotes. 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: 𝑓 0.68 ( 36746 hom., cov: 34)
Exomes 𝑓: 0.59 ( 104995 hom. )

Consequence

CPEB3
ENST00000265997.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CPEB3NM_014912.5 linkuse as main transcriptc.1454-115C>T intron_variant ENST00000265997.5 NP_055727.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CPEB3ENST00000265997.5 linkuse as main transcriptc.1454-115C>T intron_variant 1 NM_014912.5 ENSP00000265997 Q8NE35-1
CPEB3ENST00000412050.8 linkuse as main transcriptc.1412-115C>T intron_variant 1 ENSP00000398310 P1Q8NE35-2
CPEB3ENST00000614585.4 linkuse as main transcriptc.1454-115C>T intron_variant 5 ENSP00000482128 Q8NE35-1

Frequencies

GnomAD3 genomes
AF:
0.679
AC:
103337
AN:
152122
Hom.:
36709
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.886
Gnomad AMI
AF:
0.488
Gnomad AMR
AF:
0.717
Gnomad ASJ
AF:
0.672
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.434
Gnomad FIN
AF:
0.482
Gnomad MID
AF:
0.693
Gnomad NFE
AF:
0.607
Gnomad OTH
AF:
0.708
GnomAD4 exome
AF:
0.589
AC:
348794
AN:
592664
Hom.:
104995
AF XY:
0.581
AC XY:
184128
AN XY:
316896
show subpopulations
Gnomad4 AFR exome
AF:
0.889
Gnomad4 AMR exome
AF:
0.708
Gnomad4 ASJ exome
AF:
0.655
Gnomad4 EAS exome
AF:
0.504
Gnomad4 SAS exome
AF:
0.443
Gnomad4 FIN exome
AF:
0.488
Gnomad4 NFE exome
AF:
0.603
Gnomad4 OTH exome
AF:
0.615
GnomAD4 genome
AF:
0.679
AC:
103433
AN:
152240
Hom.:
36746
Cov.:
34
AF XY:
0.668
AC XY:
49734
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.886
Gnomad4 AMR
AF:
0.715
Gnomad4 ASJ
AF:
0.672
Gnomad4 EAS
AF:
0.528
Gnomad4 SAS
AF:
0.434
Gnomad4 FIN
AF:
0.482
Gnomad4 NFE
AF:
0.607
Gnomad4 OTH
AF:
0.709
Alfa
AF:
0.619
Hom.:
14038
Bravo
AF:
0.714
Asia WGS
AF:
0.499
AC:
1739
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.81
DANN
Benign
0.40

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs701846; hg19: chr10-93871066; API