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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030627.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CPEB4	NM_030627.4	MANE Select	c.1208-122A>G	intron	N/A	NP_085130.2	Q17RY0-1
CPEB4	NM_001308189.2		c.1208-10698A>G	intron	N/A	NP_001295118.1	Q17RY0-2
CPEB4	NM_001308191.2		c.1208-12639A>G	intron	N/A	NP_001295120.1	B7ZLQ8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CPEB4	ENST00000265085.10	TSL:1 MANE Select	c.1208-122A>G	intron	N/A	ENSP00000265085.5	Q17RY0-1
CPEB4	ENST00000334035.9	TSL:1	c.1208-10698A>G	intron	N/A	ENSP00000334533.5	Q17RY0-2
CPEB4	ENST00000520867.5	TSL:1	c.1208-12639A>G	intron	N/A	ENSP00000429092.1	B7ZLQ8

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over