rs2216630

Positions:

• chr4-77248002-G-A
• chr4-77248002-G-C

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 0.237 in 151,378 control chromosomes in the GnomAD database, including 5,013 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 0.24 (5013 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

CCNG2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.77248002G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1675+55735G>A		intron_variant		1
CCNG2	ENST00000514756.1	n.101+55735G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35885 AN: 151278 Hom.: 5021 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.237 AC: 35861 AN: 151378 Hom.: 5013 Cov.: 31 AF XY: 0.232 AC XY: 17098 AN XY: 73854

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.251

Alfa AF: 0.292 Hom.: 2897

Bravo AF: 0.228

Asia WGS AF: 0.0840 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2216630; hg19: chr4-78169155;