8-22606110-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001393997.1(CCAR2):c.84C>T(p.Gly28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,610,666 control chromosomes in the GnomAD database, including 82,545 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 7230 hom., cov: 32)
Exomes 𝑓: 0.32 ( 75315 hom. )
Consequence
CCAR2
NM_001393997.1 synonymous
NM_001393997.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.00
Genes affected
CCAR2 (HGNC:23360): (cell cycle and apoptosis regulator 2) Enables RNA polymerase II complex binding activity and enzyme inhibitor activity. Involved in several processes, including regulation of cellular protein metabolic process; regulation of signal transduction; and regulation of transcription, DNA-templated. Located in several cellular components, including mitochondrial matrix; nucleoplasm; and spindle. Part of DBIRD complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 8-22606110-C-T is Benign according to our data. Variant chr8-22606110-C-T is described in ClinVar as [Benign]. Clinvar id is 3059932.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCAR2 | NM_001393997.1 | c.84C>T | p.Gly28= | synonymous_variant | 3/21 | ENST00000308511.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCAR2 | ENST00000308511.9 | c.84C>T | p.Gly28= | synonymous_variant | 3/21 | 1 | NM_001393997.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.303 AC: 45946AN: 151880Hom.: 7225 Cov.: 32
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GnomAD3 exomes AF: 0.300 AC: 75312AN: 251446Hom.: 11681 AF XY: 0.306 AC XY: 41612AN XY: 135892
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GnomAD4 exome AF: 0.319 AC: 465832AN: 1458668Hom.: 75315 Cov.: 35 AF XY: 0.322 AC XY: 233582AN XY: 725864
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GnomAD4 genome AF: 0.302 AC: 45974AN: 151998Hom.: 7230 Cov.: 32 AF XY: 0.298 AC XY: 22128AN XY: 74262
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CCAR2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at