rs9307270

Positions:

• chr4-77385265-A-G

Variant summary

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

The variant allele was found at a frequency of 0.0872 in 152,240 control chromosomes in the GnomAD database, including 658 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 0.087 (658 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

CCNG2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.77385265A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1676-46975A>G		intron_variant		1
CCNG2	ENST00000514756.1	n.232+498A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13273 AN: 152122 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0872 AC: 13271 AN: 152240 Hom.: 658 Cov.: 32 AF XY: 0.0906 AC XY: 6746 AN XY: 74424

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0917

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0951 Hom.: 428

Bravo AF: 0.0829

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307270; hg19: chr4-78306419;