dbSNP rs17763373: CPEB4:c.1208-122A>G (chr5-173932328-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030627.4(CPEB4):c.1208-122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 626,444 control chromosomes in the GnomAD database, including 969 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 0.042 ( 185 hom., cov: 33)

Exomes 𝑓: 0.051 ( 784 hom. )

Consequence

CPEB4
NM_030627.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0940

Publications

10 publications found

Variant links:

Genes affected

CPEB4 (HGNC:21747): (cytoplasmic polyadenylation element binding protein 4) Enables RNA binding activity. Predicted to be involved in several processes, including cellular response to glucose starvation; negative regulation of cytoplasmic translation; and response to ischemia. Located in cytoplasm and nucleus. Biomarker of liver cirrhosis; portal hypertension; and primary biliary cholangitis. [provided by Alliance of Genome Resources, Apr 2022]

CPEB4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB4	NM_030627.4 link	c.1208-122A>G		intron_variant	Intron 2 of 9	ENST00000265085.10	NP_085130.2	Q17RY0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB4	ENST00000265085.10 link	c.1208-122A>G		intron_variant	Intron 2 of 9	1	NM_030627.4	ENSP00000265085.5		Q17RY0-1

Frequencies

GnomAD3 genomes

AF:

0.0424

AC:

6448

AN:

152172

Hom.:

185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0112

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.0476

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00620

Gnomad FIN

AF:

0.0400

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0634

Gnomad OTH

AF:

0.0526

GnomAD4 exome

AF:

0.0514

AC:

24391

AN:

474154

Hom.:

784

AF XY:

0.0501

AC XY:

12654

AN XY:

252444

show subpopulations

African (AFR)

AF:

0.0110

AC:

127

AN:

11534

American (AMR)

AF:

0.0396

AC:

604

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0655

AC:

887

AN:

13546

East Asian (EAS)

AF:

0.000104

AC:

AN:

28948

South Asian (SAS)

AF:

0.00820

AC:

310

AN:

37800

European-Finnish (FIN)

AF:

0.0421

AC:

1806

AN:

42910

Middle Eastern (MID)

AF:

0.0333

AC:

AN:

2040

European-Non Finnish (NFE)

AF:

0.0651

AC:

19297

AN:

296250

Other (OTH)

AF:

0.0498

AC:

1289

AN:

25864

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1114

2229

3343

4458

5572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

204

408

612

816

1020

<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

AF:

0.0423

AC:

6448

AN:

152290

Hom.:

185

Cov.:

AF XY:

0.0411

AC XY:

3057

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0111

AC:

462

AN:

41580

American (AMR)

AF:

0.0475

AC:

727

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0706

AC:

245

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00662

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0400

AC:

424

AN:

10610

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0634

AC:

4308

AN:

67992

Other (OTH)

AF:

0.0521

AC:

110

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

320

640

960

1280

1600

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0545

Hom.:

664

Bravo

AF:

0.0418

Asia WGS

AF:

0.00376

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.0

(source)

DANN

Benign

0.76

PhyloP100

-0.094

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over