rs3743203

Positions:

• chr15-55356764-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

DNAAF4-CCPG1 (HGNC:):

ACMG classification

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: 33311 AN: 151902 Hom.: 4179 Cov.: 32

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.: 30 AF XY: 0.186 AC XY: 73900 AN XY: 397998

Gnomad4 AFR exome AF: 0.249

Gnomad4 AMR exome AF: 0.298

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.529

Gnomad4 SAS exome AF: 0.277

Gnomad4 FIN exome AF: 0.135

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.219 AC: 33327 AN: 152020 Hom.: 4181 Cov.: 32 AF XY: 0.221 AC XY: 16386 AN XY: 74304

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.228

Alfa AF: 0.191 Hom.: 1717

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
DANN	Benign	0.49

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

LitVar

Other links and lift over

dbSNP: rs3743203; hg19: chr15-55648962;