4-77215780-G-T

Position:

• chr4-77215780-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNG2	ENST00000497512.5	n.1675+23513G>T		intron_variant, non_coding_transcript_variant		1
CCNG2	ENST00000514756.1	n.101+23513G>T		intron_variant, non_coding_transcript_variant		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;