17-40289585-C-T
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001254.4(CDC6):c.165C>T(p.Pro55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,613,974 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 3 hom., cov: 31)
Exomes 𝑓: 0.0016 ( 12 hom. )
Consequence
CDC6
NM_001254.4 synonymous
NM_001254.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.208
Genes affected
CDC6 (HGNC:1744): (cell division cycle 6) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Cdc6, a protein essential for the initiation of DNA replication. This protein functions as a regulator at the early steps of DNA replication. It localizes in cell nucleus during cell cyle G1, but translocates to the cytoplasm at the start of S phase. The subcellular translocation of this protein during cell cyle is regulated through its phosphorylation by Cdks. Transcription of this protein was reported to be regulated in response to mitogenic signals through transcriptional control mechanism involving E2F proteins. [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=-0.31).
BP6
Variant 17-40289585-C-T is Benign according to our data. Variant chr17-40289585-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 210619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-40289585-C-T is described in Lovd as [Benign]. Variant chr17-40289585-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.208 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0016 (2339/1461724) while in subpopulation MID AF= 0.0199 (115/5768). AF 95% confidence interval is 0.017. There are 12 homozygotes in gnomad4_exome. There are 1330 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC6 | NM_001254.4 | c.165C>T | p.Pro55= | synonymous_variant | 2/12 | ENST00000209728.9 | NP_001245.1 | |
CDC6 | XM_011525541.3 | c.165C>T | p.Pro55= | synonymous_variant | 2/13 | XP_011523843.1 | ||
CDC6 | XM_011525542.2 | c.165C>T | p.Pro55= | synonymous_variant | 2/13 | XP_011523844.1 | ||
CDC6 | XM_047437207.1 | c.165C>T | p.Pro55= | synonymous_variant | 2/12 | XP_047293163.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC6 | ENST00000209728.9 | c.165C>T | p.Pro55= | synonymous_variant | 2/12 | 1 | NM_001254.4 | ENSP00000209728 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 152132Hom.: 3 Cov.: 31
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GnomAD3 exomes AF: 0.00221 AC: 556AN: 251396Hom.: 3 AF XY: 0.00252 AC XY: 342AN XY: 135890
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GnomAD4 exome AF: 0.00160 AC: 2339AN: 1461724Hom.: 12 Cov.: 31 AF XY: 0.00183 AC XY: 1330AN XY: 727170
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GnomAD4 genome AF: 0.00122 AC: 185AN: 152250Hom.: 3 Cov.: 31 AF XY: 0.00121 AC XY: 90AN XY: 74452
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | CDC6: BP4, BP7, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 06, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Meier-Gorlin syndrome 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at