4-77164408-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_004354.3(CCNG2):c.840C>T(p.Leu280Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00159 in 1,614,042 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0085 ( 22 hom., cov: 32)
Exomes 𝑓: 0.00087 ( 15 hom. )
Consequence
CCNG2
NM_004354.3 synonymous
NM_004354.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.622
Genes affected
CCNG2 (HGNC:1593): (cyclin G2) The eukaryotic cell cycle is governed by cyclin-dependent protein kinases (CDKs) whose activities are regulated by cyclins and CDK inhibitors. The 8 species of cyclins reported in mammals, cyclins A through H, share a conserved amino acid sequence of about 90 residues called the cyclin box. The amino acid sequence of cyclin G is well conserved among mammals. The nucleotide sequence of cyclin G1 and cyclin G2 are 53% identical. Unlike cyclin G1, cyclin G2 contains a C-terminal PEST protein destabilization motif, suggesting that cyclin G2 expression is tightly regulated through the cell cycle. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 4-77164408-C-T is Benign according to our data. Variant chr4-77164408-C-T is described in ClinVar as [Benign]. Clinvar id is 708394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.622 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00853 (1298/152190) while in subpopulation AFR AF= 0.0298 (1237/41496). AF 95% confidence interval is 0.0284. There are 22 homozygotes in gnomad4. There are 598 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1298 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCNG2 | NM_004354.3 | c.840C>T | p.Leu280Leu | synonymous_variant | Exon 7 of 8 | ENST00000316355.10 | NP_004345.1 | |
CCNG2 | XM_011532398.2 | c.840C>T | p.Leu280Leu | synonymous_variant | Exon 7 of 8 | XP_011530700.1 | ||
CCNG2 | XM_011532399.3 | c.840C>T | p.Leu280Leu | synonymous_variant | Exon 7 of 8 | XP_011530701.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00850 AC: 1293AN: 152072Hom.: 21 Cov.: 32
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GnomAD3 exomes AF: 0.00208 AC: 522AN: 251432Hom.: 8 AF XY: 0.00159 AC XY: 216AN XY: 135894
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GnomAD4 exome AF: 0.000867 AC: 1267AN: 1461852Hom.: 15 Cov.: 31 AF XY: 0.000737 AC XY: 536AN XY: 727232
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GnomAD4 genome AF: 0.00853 AC: 1298AN: 152190Hom.: 22 Cov.: 32 AF XY: 0.00804 AC XY: 598AN XY: 74416
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Oct 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at