rs1550601

Positions:

• chr4-77414092-A-G

Variant summary

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

The ENST00000497512.5(CCNG2):​n.1676-18148A>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 0.369 in 152,102 control chromosomes in the GnomAD database, including 10,711 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 (10711 hom., cov: 32)
• Consequence: CCNG2 ENST00000497512.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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.1676-18148A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000513871.1	n.123-14298T>C		intron_variant, non_coding_transcript_variant		4
CCNG2	ENST00000514756.1	n.233-17634A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56088 AN: 151982 Hom.: 10696 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.369 AC: 56154 AN: 152102 Hom.: 10711 Cov.: 32 AF XY: 0.372 AC XY: 27636 AN XY: 74360

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.352

Alfa AF: 0.347 Hom.: 4758

Bravo AF: 0.361

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1550601; hg19: chr4-78335246;