rs3743203
Positions:
Variant summary
Our verdict is Benign. Variant got -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
ENST00000310958.10 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.237
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]
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=-0.92).
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCPG1 | NM_001204450.2 | c.2235-355A>G | intron_variant | ENST00000442196.8 | |||
DNAAF4-CCPG1 | NR_037923.1 | n.3652-355A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCPG1 | ENST00000442196.8 | c.2235-355A>G | intron_variant | 2 | NM_001204450.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.219 AC: 33311AN: 151902Hom.: 4179 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
33311
AN:
151902
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.186 AC: 159473AN: 858478Hom.: 15547 Cov.: 30 AF XY: 0.186 AC XY: 73900AN XY: 397998
GnomAD4 exome
AF:
AC:
159473
AN:
858478
Hom.:
Cov.:
30
AF XY:
AC XY:
73900
AN XY:
397998
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.219 AC: 33327AN: 152020Hom.: 4181 Cov.: 32 AF XY: 0.221 AC XY: 16386AN XY: 74304
GnomAD4 genome
?
AF:
AC:
33327
AN:
152020
Hom.:
Cov.:
32
AF XY:
AC XY:
16386
AN XY:
74304
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1333
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at