rs2216630

Positions:

• chr4-77248002-G-A
• chr4-77248002-G-C

Variant summary

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

The ENST00000497512.5(CCNG2):​n.1675+55735G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNG2	ENST00000497512.5	n.1675+55735G>A		intron_variant, non_coding_transcript_variant		1
CCNG2	ENST00000514756.1	n.101+55735G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.251

Alfa AF: 0.292 Hom.: 2897

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2216630; hg19: chr4-78169155;