rs1442696

Variant names:

• chr4-77429910-A-G
• rs1442696
• ENST00000497512.5:n.1676-2330A>G

Variant summary

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

The ENST00000497512.5(CCNG2):​n.1676-2330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,144 control chromosomes in the GnomAD database, including 2,278 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 0.17 (2278 hom., cov: 32)
• Consequence: CCNG2 ENST00000497512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

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]

ENSG00000249036 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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.1676-2330A>G		intron_variant	Intron 10 of 11	1
ENSG00000249036	ENST00000513871.1	n.123-30116T>C		intron_variant	Intron 1 of 2	4
CCNG2	ENST00000514756.1	n.233-1816A>G		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25525 AN: 152026 Hom.: 2272 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.168 AC: 25561 AN: 152144 Hom.: 2278 Cov.: 32 AF XY: 0.168 AC XY: 12532 AN XY: 74380

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.179

Alfa AF: 0.173 Hom.: 4752

Bravo AF: 0.163

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1442696; hg19: chr4-78351064;