NM_001204450.2:c.-10+5589T>C

Variant names:

• chr15-55402632-A-G
• rs11071185
• NM_001204450.2:c.-10+5589T>C

Variant summary

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

The NM_001204450.2(CCPG1):​c.-10+5589T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,130 control chromosomes in the GnomAD database, including 9,018 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 0.32 (9018 hom., cov: 33)
• Consequence: CCPG1 NM_001204450.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCPG1	NM_001204450.2	c.-10+5589T>C		intron_variant	Intron 1 of 8	ENST00000442196.8	NP_001191379.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCPG1	ENST00000442196.8	c.-10+5589T>C		intron_variant	Intron 1 of 8	2	NM_001204450.2	ENSP00000403400.3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48762 AN: 152010 Hom.: 9019 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.321 AC: 48767 AN: 152130 Hom.: 9018 Cov.: 33 AF XY: 0.317 AC XY: 23549 AN XY: 74370

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.327

Alfa AF: 0.375 Hom.: 5008

Bravo AF: 0.304

Asia WGS AF: 0.269 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.010
DANN	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11071185; hg19: chr15-55694830;