rs3743203

Variant names:

• chr15-55356764-T-C
• rs3743203
• ENST00000310958.10:c.*2735A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004748.6(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 NM_004748.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 10 publications found

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: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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004748.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCPG1	NM_001204450.2	MANE Select	c.2235-355A>G		intron	N/A	NP_001191379.1	Q9ULG6-5
	CCPG1	NM_004748.6		c.*2735A>G		3_prime_UTR	Exon 8 of 8	NP_004739.3
	CCPG1	NM_020739.5		c.*2735A>G		3_prime_UTR	Exon 8 of 8	NP_065790.2	Q9ULG6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCPG1	ENST00000310958.10	TSL:1	c.*2735A>G		3_prime_UTR	Exon 8 of 8	ENSP00000311656.6	Q9ULG6-1
	CCPG1	ENST00000442196.8	TSL:2 MANE Select	c.2235-355A>G		intron	N/A	ENSP00000403400.3	Q9ULG6-5
	CCPG1	ENST00000946865.1		c.2331-355A>G		intron	N/A	ENSP00000616924.1

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

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

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

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: 49 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12173 AN: 67968

Other (OTH) AF: 0.228 AC: 481 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3743203; hg19: chr15-55648962;