rs10000203

Variant names:

• chr4-77355406-C-G
• rs10000203
• ENST00000497512.5:n.1676-76834C>G

Variant summary

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

The ENST00000497512.5(CCNG2):​n.1676-76834C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 151,934 control chromosomes in the GnomAD database, including 793 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 0.096 (793 hom., cov: 32)
• Consequence: CCNG2 ENST00000497512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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.1676-76834C>G		intron_variant	Intron 10 of 11	1
CCNG2	ENST00000514756.1	n.102-29231C>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0955 AC: 14504 AN: 151830 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0956 AC: 14532 AN: 151934 Hom.: 793 Cov.: 32 AF XY: 0.0995 AC XY: 7385 AN XY: 74220

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0853 Hom.: 56

Bravo AF: 0.0939

Asia WGS AF: 0.180 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10000203; hg19: chr4-78276559;