4-77355406-C-G

Position:

• chr4-77355406-C-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 0.0956 in 151,934 control chromosomes in the GnomAD database, including 793 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 0.096 (793 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

CCNG2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.77355406C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1676-76834C>G		intron_variant		1
CCNG2	ENST00000514756.1	n.102-29231C>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0955 AC: 14504 AN: 151830 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0956 AC: 14532 AN: 151934 Hom.: 793 Cov.: 32 AF XY: 0.0995 AC XY: 7385 AN XY: 74220

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0853 Hom.: 56

Bravo AF: 0.0939

Asia WGS AF: 0.180 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10000203; hg19: chr4-78276559;