dbSNP rs11186856: CPEB3:c.1006-11624T>C (chr10-92204260-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_014912.5(CPEB3):c.1006-11624T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 148,354 control chromosomes in the GnomAD database, including 5,052 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 0.24 ( 5049 hom., cov: 32)

Exomes 𝑓: 0.57 ( 3 hom. )

Consequence

CPEB3
NM_014912.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.90

Publications

8 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)

CPEB3 links:

ENSG00000221042 (HGNC:):

ENSG00000221042 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB3	NM_014912.5 link	c.1006-11624T>C		intron_variant	Intron 2 of 9	ENST00000265997.5	NP_055727.3	Q8NE35-1B3KXC1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CPEB3	ENST00000265997.5 link	c.1006-11624T>C	intron_variant	Intron 2 of 9	1	NM_014912.5	ENSP00000265997.4	Q8NE35-1
CPEB3	ENST00000412050.8 link	c.1006-11624T>C	intron_variant	Intron 2 of 9	1		ENSP00000398310.2	Q8NE35-2
ENSG00000221042	ENST00000408115.1 link	n.47T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
CPEB3	ENST00000614585.4 link	c.1006-11624T>C	intron_variant	Intron 2 of 9	5		ENSP00000482128.1	Q8NE35-1

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

36295

AN:

148222

Hom.:

5054

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.316

Gnomad OTH

AF:

0.289

GnomAD4 exome

AF:

0.571

AC:

AN:

Hom.:

Cov.:

AF XY:

0.571

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.700

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.600

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.245

AC:

36288

AN:

148340

Hom.:

5049

Cov.:

AF XY:

0.238

AC XY:

17307

AN XY:

72590

show subpopulations

African (AFR)

AF:

0.122

AC:

4611

AN:

37936

American (AMR)

AF:

0.273

AC:

4115

AN:

15092

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

1300

AN:

3468

East Asian (EAS)

AF:

0.135

AC:

698

AN:

5178

South Asian (SAS)

AF:

0.122

AC:

587

AN:

4826

European-Finnish (FIN)

AF:

0.235

AC:

2482

AN:

10578

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.316

AC:

21501

AN:

67974

Other (OTH)

AF:

0.289

AC:

601

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1381

2762

4142

5523

6904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.287

Hom.:

3298

Bravo

AF:

0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

2.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over