chr4-77248002-G-A

Variant names:

• chr4-77248002-G-A
• rs2216630
• ENST00000497512.5:n.1675+55735G>A

Variant summary

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

The ENST00000497512.5(CCNG2):​n.1675+55735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,378 control chromosomes in the GnomAD database, including 5,013 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 0.24 (5013 hom., cov: 31)
• Consequence: CCNG2 ENST00000497512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 1 publications found

Genes affected

CCNG2 (HGNC:1593): (cyclin G2) The eukaryotic cell cycle is governed by cyclin-dependent protein kinases (CDKs) whose activities are regulated by cyclins and CDK inhibitors. The 8 species of cyclins reported in mammals, cyclins A through H, share a conserved amino acid sequence of about 90 residues called the cyclin box. The amino acid sequence of cyclin G is well conserved among mammals. The nucleotide sequence of cyclin G1 and cyclin G2 are 53% identical. Unlike cyclin G1, cyclin G2 contains a C-terminal PEST protein destabilization motif, suggesting that cyclin G2 expression is tightly regulated through the cell cycle. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1675+55735G>A		intron_variant	Intron 10 of 11	1
CCNG2	ENST00000514756.1	n.101+55735G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35885 AN: 151278 Hom.: 5021 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.237 AC: 35861 AN: 151378 Hom.: 5013 Cov.: 31 AF XY: 0.232 AC XY: 17098 AN XY: 73854

African (AFR) AF: 0.113 AC: 4678 AN: 41254

American (AMR) AF: 0.242 AC: 3687 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1415 AN: 3462

East Asian (EAS) AF: 0.0134 AC: 69 AN: 5136

South Asian (SAS) AF: 0.183 AC: 874 AN: 4784

European-Finnish (FIN) AF: 0.292 AC: 3030 AN: 10370

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21193 AN: 67852

Other (OTH) AF: 0.251 AC: 525 AN: 2092

Alfa AF: 0.292 Hom.: 3269

Bravo AF: 0.228

Asia WGS AF: 0.0840 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.42
PhyloP100		-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2216630; hg19: chr4-78169155;