Variant 16-88807382-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_030928.4(CDT1):c.1377C>T(p.Arg459Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 1,612,690 control chromosomes in the GnomAD database, including 2,834 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 267 hom., cov: 34)

Exomes 𝑓: 0.054 ( 2567 hom. )

Consequence

CDT1
NM_030928.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -3.34

Variant links:

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]

CDT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 16-88807382-C-T is Benign according to our data. Variant chr16-88807382-C-T is described in ClinVar as [Benign]. Clinvar id is 128669.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.067 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDT1	NM_030928.4 linkuse as main transcript	c.1377C>T	p.Arg459Arg	synonymous_variant	9/10	ENST00000301019.9	NP_112190.2	Q9H211

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDT1	ENST00000301019.9 linkuse as main transcript	c.1377C>T	p.Arg459Arg	synonymous_variant	9/10	1	NM_030928.4	ENSP00000301019.4		Q9H211
CDT1	ENST00000569140.1 linkuse as main transcript	c.*40C>T		downstream_gene_variant		3		ENSP00000456926.1		H3BSY1

Frequencies

GnomAD3 genomes

AF:

0.0564

AC:

8585

AN:

152240

Hom.:

267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0558

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0554

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.0246

Gnomad SAS

AF:

0.0734

Gnomad FIN

AF:

0.0378

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0566

Gnomad OTH

AF:

0.0684

GnomAD3 exomes

AF:

0.0555

AC:

13781

AN:

248160

Hom.:

493

AF XY:

0.0577

AC XY:

7799

AN XY:

135070

show subpopulations

Gnomad AFR exome

AF:

0.0511

Gnomad AMR exome

AF:

0.0370

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.0249

Gnomad SAS exome

AF:

0.0790

Gnomad FIN exome

AF:

0.0355

Gnomad NFE exome

AF:

0.0565

Gnomad OTH exome

AF:

0.0620

GnomAD4 exome

AF:

0.0543

AC:

79333

AN:

1460332

Hom.:

2567

Cov.:

AF XY:

0.0559

AC XY:

40607

AN XY:

726484

show subpopulations

Gnomad4 AFR exome

AF:

0.0572

Gnomad4 AMR exome

AF:

0.0414

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.0184

Gnomad4 SAS exome

AF:

0.0827

Gnomad4 FIN exome

AF:

0.0347

Gnomad4 NFE exome

AF:

0.0523

Gnomad4 OTH exome

AF:

0.0587

GnomAD4 genome

AF:

0.0564

AC:

8593

AN:

152358

Hom.:

267

Cov.:

AF XY:

0.0565

AC XY:

4209

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.0560

Gnomad4 AMR

AF:

0.0553

Gnomad4 ASJ

AF:

0.136

Gnomad4 EAS

AF:

0.0245

Gnomad4 SAS

AF:

0.0733

Gnomad4 FIN

AF:

0.0378

Gnomad4 NFE

AF:

0.0566

Gnomad4 OTH

AF:

0.0676

Alfa

AF:

0.0507

Hom.:

136

Bravo

AF:

0.0564

Asia WGS

AF:

0.0440

AC:

154

AN:

3478

EpiCase

AF:

0.0632

EpiControl

AF:

0.0653

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

not specified

Benign:2

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. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

1.3

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over