4-77420506-T-C

Variant names:

• chr4-77420506-T-C
• rs7677281
• ENST00000497512.5:n.1676-11734T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000497512.5(CCNG2):​n.1676-11734T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,120 control chromosomes in the GnomAD database, including 38,982 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 0.71 (38982 hom., cov: 32)
• Consequence: CCNG2 ENST00000497512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497512.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNG2	ENST00000497512.5	TSL:1	n.1676-11734T>C		intron	N/A
	ENSG00000249036	ENST00000513871.1	TSL:4	n.123-20712A>G		intron	N/A
	CCNG2	ENST00000514756.1	TSL:4	n.233-11220T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108562 AN: 152002 Hom.: 38936 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.714 AC: 108662 AN: 152120 Hom.: 38982 Cov.: 32 AF XY: 0.709 AC XY: 52755 AN XY: 74364

African (AFR) AF: 0.678 AC: 28116 AN: 41496

American (AMR) AF: 0.680 AC: 10396 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3016 AN: 5162

South Asian (SAS) AF: 0.603 AC: 2901 AN: 4814

European-Finnish (FIN) AF: 0.716 AC: 7580 AN: 10588

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51918 AN: 67982

Other (OTH) AF: 0.722 AC: 1525 AN: 2112

Alfa AF: 0.737 Hom.: 30798

Bravo AF: 0.709

Asia WGS AF: 0.591 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7677281; hg19: chr4-78341660;