NM_004060.4:c.264+669T>C

Variant names:

• chr5-163440189-T-C
• rs2069347
• NM_004060.4:c.264+669T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004060.4(CCNG1):​c.264+669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,864 control chromosomes in the GnomAD database, including 13,310 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 0.41 (13310 hom., cov: 31)
• Consequence: CCNG1 NM_004060.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 13 publications found

Genes affected

CCNG1 (HGNC:1592): (cyclin G1) The eukaryotic cell cycle is governed by cyclin-dependent protein kinases (CDKs) whose activities are regulated by cyclins and CDK inhibitors. The protein encoded by this gene is a member of the cyclin family and contains the cyclin box. The encoded protein lacks the protein destabilizing (PEST) sequence that is present in other family members. Transcriptional activation of this gene can be induced by tumor protein p53. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNG1	NM_004060.4	c.264+669T>C		intron_variant	Intron 2 of 6	ENST00000340828.7	NP_004051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNG1	ENST00000340828.7	c.264+669T>C		intron_variant	Intron 2 of 6	1	NM_004060.4	ENSP00000344635.2
CCNG1	ENST00000510664.5	c.13+843T>C		intron_variant	Intron 2 of 6	5		ENSP00000422379.1
CCNG1	ENST00000511490.4	c.264+669T>C		intron_variant	Intron 3 of 3	5		ENSP00000421132.2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62145 AN: 151746 Hom.: 13307 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.409 AC: 62160 AN: 151864 Hom.: 13310 Cov.: 31 AF XY: 0.404 AC XY: 29961 AN XY: 74236

African (AFR) AF: 0.307 AC: 12696 AN: 41408

American (AMR) AF: 0.443 AC: 6759 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3468

East Asian (EAS) AF: 0.181 AC: 934 AN: 5172

South Asian (SAS) AF: 0.285 AC: 1371 AN: 4816

European-Finnish (FIN) AF: 0.430 AC: 4521 AN: 10524

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33048 AN: 67914

Other (OTH) AF: 0.428 AC: 902 AN: 2108

Alfa AF: 0.458 Hom.: 68671

Bravo AF: 0.409

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.42
PhyloP100		0.092
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2069347; hg19: chr5-162867195;