chr4-77215780-G-T

Variant names:

• chr4-77215780-G-T
• rs11937061
• ENST00000497512.5:n.1675+23513G>T

Variant summary

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

The ENST00000497512.5(CCNG2):​n.1675+23513G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,976 control chromosomes in the GnomAD database, including 10,796 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 0.37 (10796 hom., cov: 32)
• Consequence: CCNG2 ENST00000497512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 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+23513G>T		intron_variant	Intron 10 of 11	1
CCNG2	ENST00000514756.1	n.101+23513G>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56727 AN: 151858 Hom.: 10791 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.373 AC: 56753 AN: 151976 Hom.: 10796 Cov.: 32 AF XY: 0.372 AC XY: 27664 AN XY: 74272

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.373

Alfa AF: 0.371 Hom.: 19756

Bravo AF: 0.372

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11937061; hg19: chr4-78136933;