rs510862
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_030928.4(CDT1):āc.915T>Cā(p.His305=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 1,598,186 control chromosomes in the GnomAD database, including 508,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.84 ( 54038 hom., cov: 35)
Exomes š: 0.79 ( 454843 hom. )
Consequence
CDT1
NM_030928.4 synonymous
NM_030928.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.92
Genes affected
CDT1 (HGNC:24576): (chromatin licensing and DNA replication factor 1) The protein encoded by this gene is involved in the formation of the pre-replication complex that is necessary for DNA replication. The encoded protein can bind geminin, which prevents replication and may function to prevent this protein from initiating replication at inappropriate origins. Phosphorylation of this protein by cyclin A-dependent kinases results in degradation of the protein. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant 16-88806103-T-C is Benign according to our data. Variant chr16-88806103-T-C is described in ClinVar as [Benign]. Clinvar id is 128683.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-88806103-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-4.92 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDT1 | NM_030928.4 | c.915T>C | p.His305= | synonymous_variant | 6/10 | ENST00000301019.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDT1 | ENST00000301019.9 | c.915T>C | p.His305= | synonymous_variant | 6/10 | 1 | NM_030928.4 | P1 | |
CDT1 | ENST00000569140.1 | c.186T>C | p.His62= | synonymous_variant | 2/5 | 3 | |||
CDT1 | ENST00000562747.1 | n.621T>C | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.839 AC: 127616AN: 152128Hom.: 53983 Cov.: 35
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GnomAD3 exomes AF: 0.801 AC: 181848AN: 227080Hom.: 73454 AF XY: 0.804 AC XY: 99814AN XY: 124128
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GnomAD4 exome AF: 0.792 AC: 1144914AN: 1445940Hom.: 454843 Cov.: 55 AF XY: 0.794 AC XY: 570749AN XY: 718954
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GnomAD4 genome ? AF: 0.839 AC: 127726AN: 152246Hom.: 54038 Cov.: 35 AF XY: 0.835 AC XY: 62185AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Meier-Gorlin syndrome 4 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Computational scores
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Name
Calibrated prediction
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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