chr4-77414092-A-G

Position:

• chr4-77414092-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 0.369 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

CCNG2 (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	Protein	UniProt
		n.77414092A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1676-18148A>G		intron_variant		1
ENSG00000249036	ENST00000513871.1	n.123-14298T>C		intron_variant		4
CCNG2	ENST00000514756.1	n.233-17634A>G		intron_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;