dbSNP rs3743203: CCPG1:c.*2735A>G (chr15-55356764-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000310958.10(CCPG1):c.*2735A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,010,498 control chromosomes in the GnomAD database, including 19,728 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 0.22 ( 4181 hom., cov: 32)

Exomes 𝑓: 0.19 ( 15547 hom. )

Consequence

CCPG1
ENST00000310958.10 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.237

Publications

10 publications found

Variant links:

Genes affected

CCPG1 (HGNC:24227): (cell cycle progression 1) Involved in positive regulation of cell cycle and positive regulation of cell population proliferation. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCPG1 links:

DNAAF4-CCPG1 (HGNC:43019): (DNAAF4-CCPG1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring dyslexia susceptibility 1 candidate 1 (DYX1C1) and cell cycle progression 1 (CCPG1) genes on chromosome 15. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]

DNAAF4-CCPG1 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCPG1	NM_001204450.2 link	c.2235-355A>G		intron_variant	Intron 8 of 8	ENST00000442196.8	NP_001191379.1	Q9ULG6-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCPG1	ENST00000442196.8 link	c.2235-355A>G		intron_variant	Intron 8 of 8	2	NM_001204450.2	ENSP00000403400.3		Q9ULG6-5

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33311

AN:

151902

Hom.:

4179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.267

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.537

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.229

GnomAD4 exome

AF:

0.186

AC:

159473

AN:

858478

Hom.:

15547

Cov.:

AF XY:

0.186

AC XY:

73900

AN XY:

397998

show subpopulations

African (AFR)

AF:

0.249

AC:

4122

AN:

16552

American (AMR)

AF:

0.298

AC:

590

AN:

1978

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

1030

AN:

6004

East Asian (EAS)

AF:

0.529

AC:

2488

AN:

4702

South Asian (SAS)

AF:

0.277

AC:

4931

AN:

17794

European-Finnish (FIN)

AF:

0.135

AC:

183

AN:

1352

Middle Eastern (MID)

AF:

0.177

AC:

302

AN:

1706

European-Non Finnish (NFE)

AF:

0.179

AC:

139661

AN:

779508

Other (OTH)

AF:

0.213

AC:

6166

AN:

28882

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

6912

13824

20735

27647

34559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6736

13472

20208

26944

33680

<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:

0.219

AC:

33327

AN:

152020

Hom.:

4181

Cov.:

AF XY:

0.221

AC XY:

16386

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.245

AC:

10160

AN:

41456

American (AMR)

AF:

0.268

AC:

4084

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

625

AN:

3470

East Asian (EAS)

AF:

0.537

AC:

2769

AN:

5154

South Asian (SAS)

AF:

0.291

AC:

1401

AN:

4808

European-Finnish (FIN)

AF:

0.127

AC:

1342

AN:

10580

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.179

AC:

12173

AN:

67968

Other (OTH)

AF:

0.228

AC:

481

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1253

2506

3758

5011

6264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.199

Hom.:

2650

Bravo

AF:

0.234

Asia WGS

AF:

0.383

AC:

1333

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

(source)

DANN

Benign

0.49

PhyloP100

-0.24

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