Variant rs3218722 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030928.4(CDT1):c.933+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 1,576,550 control chromosomes in the GnomAD database, including 7,723 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 2761 hom., cov: 34)

Exomes 𝑓: 0.065 ( 4962 hom. )

Consequence

CDT1
NM_030928.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -6.47

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 16-88806134-C-T is Benign according to our data. Variant chr16-88806134-C-T is described in ClinVar as [Benign]. Clinvar id is 261939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDT1	NM_030928.4 linkuse as main transcript	c.933+13C>T		intron_variant		ENST00000301019.9

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
CDT1	ENST00000301019.9 linkuse as main transcript	c.933+13C>T	intron_variant		1	NM_030928.4	P1
CDT1	ENST00000569140.1 linkuse as main transcript	c.203+13C>T	intron_variant		3
CDT1	ENST00000562747.1 linkuse as main transcript	n.652C>T	non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21235

AN:

152184

Hom.:

2753

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0872

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0233

Gnomad SAS

AF:

0.0841

Gnomad FIN

AF:

0.0377

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.0576

Gnomad OTH

AF:

0.135

GnomAD3 exomes

AF:

0.0847

AC:

16667

AN:

196808

Hom.:

1310

AF XY:

0.0814

AC XY:

8738

AN XY:

107394

show subpopulations

Gnomad AFR exome

AF:

0.369

Gnomad AMR exome

AF:

0.0559

Gnomad ASJ exome

AF:

0.150

Gnomad EAS exome

AF:

0.0255

Gnomad SAS exome

AF:

0.0932

Gnomad FIN exome

AF:

0.0384

Gnomad NFE exome

AF:

0.0610

Gnomad OTH exome

AF:

0.0784

GnomAD4 exome

AF:

0.0646

AC:

91938

AN:

1424248

Hom.:

4962

Cov.:

AF XY:

0.0651

AC XY:

46030

AN XY:

707162

show subpopulations

Gnomad4 AFR exome

AF:

0.359

Gnomad4 AMR exome

AF:

0.0620

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.0158

Gnomad4 SAS exome

AF:

0.0940

Gnomad4 FIN exome

AF:

0.0353

Gnomad4 NFE exome

AF:

0.0531

Gnomad4 OTH exome

AF:

0.0818

GnomAD4 genome

AF:

0.140

AC:

21278

AN:

152302

Hom.:

2761

Cov.:

AF XY:

0.137

AC XY:

10215

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.343

Gnomad4 AMR

AF:

0.0870

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.0231

Gnomad4 SAS

AF:

0.0837

Gnomad4 FIN

AF:

0.0377

Gnomad4 NFE

AF:

0.0576

Gnomad4 OTH

AF:

0.133

Alfa

AF:

0.106

Hom.:

311

Bravo

AF:

0.153

Asia WGS

AF:

0.0650

AC:

226

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

not specified

Benign:1

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

-0.96

CADD

Benign

0.012

DANN

Benign

0.71

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