15-55376216-C-G

Variant names:

• chr15-55376216-C-G
• rs472579
• NM_001204450.2:c.454+733G>C

Variant summary

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

The NM_001204450.2(CCPG1):​c.454+733G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,042 control chromosomes in the GnomAD database, including 22,635 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 0.53 (22635 hom., cov: 33)
• Consequence: CCPG1 NM_001204450.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204450.2. 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.454+733G>C		intron	N/A	NP_001191379.1	Q9ULG6-5
	CCPG1	NM_004748.6		c.454+733G>C		intron	N/A	NP_004739.3
	CCPG1	NM_020739.5		c.454+733G>C		intron	N/A	NP_065790.2	Q9ULG6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCPG1	ENST00000442196.8	TSL:2 MANE Select	c.454+733G>C		intron	N/A	ENSP00000403400.3	Q9ULG6-5
	CCPG1	ENST00000310958.10	TSL:1	c.454+733G>C		intron	N/A	ENSP00000311656.6	Q9ULG6-1
	CCPG1	ENST00000568808.5	TSL:1	n.454+733G>C		intron	N/A	ENSP00000455852.1	H3BQN1

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80959 AN: 151924 Hom.: 22599 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.496

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.533 AC: 81040 AN: 152042 Hom.: 22635 Cov.: 33 AF XY: 0.524 AC XY: 38974 AN XY: 74308

African (AFR) AF: 0.685 AC: 28422 AN: 41480

American (AMR) AF: 0.386 AC: 5897 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1527 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1348 AN: 5162

South Asian (SAS) AF: 0.428 AC: 2062 AN: 4816

European-Finnish (FIN) AF: 0.451 AC: 4756 AN: 10548

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35350 AN: 67992

Other (OTH) AF: 0.495 AC: 1044 AN: 2110

Alfa AF: 0.411 Hom.: 1153

Bravo AF: 0.530

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.46
PhyloP100		0.35
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: rs472579; hg19: chr15-55668414;