rs1442696

Positions:

• chr4-77429910-A-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, non coding transcript 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, non_coding_transcript
• 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]

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1676-2330A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000513871.1	n.123-30116T>C		intron_variant, non_coding_transcript_variant		4
CCNG2	ENST00000514756.1	n.233-1816A>G		intron_variant, non_coding_transcript_variant		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;