rs587780304
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_030928.4(CDT1):c.111C>T(p.Leu37=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,401,470 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0011 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 5 hom. )
Consequence
CDT1
NM_030928.4 synonymous
NM_030928.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.184
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=-0.72).
BP6
?
Variant 16-88803942-C-T is Benign according to our data. Variant chr16-88803942-C-T is described in ClinVar as [Benign]. Clinvar id is 128660.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.184 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00109 (165/151272) while in subpopulation SAS AF= 0.00124 (6/4822). AF 95% confidence interval is 0.000719. There are 2 homozygotes in gnomad4. There are 75 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDT1 | NM_030928.4 | c.111C>T | p.Leu37= | synonymous_variant | 1/10 | ENST00000301019.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDT1 | ENST00000301019.9 | c.111C>T | p.Leu37= | synonymous_variant | 1/10 | 1 | NM_030928.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00109 AC: 165AN: 151170Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00261 AC: 157AN: 60082Hom.: 0 AF XY: 0.00248 AC XY: 88AN XY: 35470
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GnomAD4 exome AF: 0.00122 AC: 1523AN: 1250198Hom.: 5 Cov.: 31 AF XY: 0.00122 AC XY: 754AN XY: 616094
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GnomAD4 genome ? AF: 0.00109 AC: 165AN: 151272Hom.: 2 Cov.: 33 AF XY: 0.00101 AC XY: 75AN XY: 73936
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 12, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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