chr4-77215780-G-T

Position:

• chr4-77215780-G-T

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 0.373 in 151,976 control chromosomes in the GnomAD database, including 10,796 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 (10796 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

CCNG2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.77215780G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNG2	ENST00000497512.5	n.1675+23513G>T		intron_variant		1
CCNG2	ENST00000514756.1	n.101+23513G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56727 AN: 151858 Hom.: 10791 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.373 AC: 56753 AN: 151976 Hom.: 10796 Cov.: 32 AF XY: 0.372 AC XY: 27664 AN XY: 74272

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.373

Alfa AF: 0.371 Hom.: 19756

Bravo AF: 0.372

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11937061; hg19: chr4-78136933;