rs1834065

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_030928.4(CDT1):c.549A>G(p.Gly183Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 1,612,704 control chromosomes in the GnomAD database, including 8,070 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 2318 hom., cov: 34)

Exomes 𝑓: 0.072 ( 5752 hom. )

Consequence

CDT1
NM_030928.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.417

Publications

11 publications found

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 Gene-Disease associations (from GenCC):

Meier-Gorlin syndrome 4
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
Meier-Gorlin syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CDT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 16-88805500-A-G is Benign according to our data. Variant chr16-88805500-A-G is described in ClinVar as [Benign]. Clinvar id is 128679.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.417 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDT1	NM_030928.4 link	c.549A>G	p.Gly183Gly	synonymous_variant	Exon 4 of 10	ENST00000301019.9	NP_112190.2	Q9H211

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDT1	ENST00000301019.9 link	c.549A>G	p.Gly183Gly	synonymous_variant	Exon 4 of 10	1	NM_030928.4	ENSP00000301019.4		Q9H211
CDT1	ENST00000562747.1 link	n.255A>G		non_coding_transcript_exon_variant	Exon 3 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20310

AN:

152054

Hom.:

2313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0823

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.00328

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.0197

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.0665

Gnomad OTH

AF:

0.123

GnomAD2 exomes

AF:

0.0837

AC:

20894

AN:

249580

AF XY:

0.0828

show subpopulations

Gnomad AFR exome

AF:

0.323

Gnomad AMR exome

AF:

0.0512

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.00285

Gnomad FIN exome

AF:

0.0214

Gnomad NFE exome

AF:

0.0675

Gnomad OTH exome

AF:

0.0806

GnomAD4 exome

AF:

0.0724

AC:

105781

AN:

1460532

Hom.:

5752

Cov.:

AF XY:

0.0739

AC XY:

53713

AN XY:

726586

show subpopulations

African (AFR)

AF:

0.322

AC:

10786

AN:

33476

American (AMR)

AF:

0.0573

AC:

2561

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

4362

AN:

26124

East Asian (EAS)

AF:

0.00237

AC:

AN:

39694

South Asian (SAS)

AF:

0.124

AC:

10665

AN:

86256

European-Finnish (FIN)

AF:

0.0218

AC:

1140

AN:

52188

Middle Eastern (MID)

AF:

0.130

AC:

750

AN:

5768

European-Non Finnish (NFE)

AF:

0.0632

AC:

70304

AN:

1111932

Other (OTH)

AF:

0.0848

AC:

5119

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

6842

13683

20525

27366

34208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.134

AC:

20339

AN:

152172

Hom.:

2318

Cov.:

AF XY:

0.130

AC XY:

9681

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.310

AC:

12867

AN:

41494

American (AMR)

AF:

0.0821

AC:

1257

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

583

AN:

3470

East Asian (EAS)

AF:

0.00329

AC:

AN:

5174

South Asian (SAS)

AF:

0.110

AC:

530

AN:

4830

European-Finnish (FIN)

AF:

0.0197

AC:

209

AN:

10610

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0665

AC:

4522

AN:

67970

Other (OTH)

AF:

0.122

AC:

258

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

866

1733

2599

3466

4332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0960

Hom.:

1663

Bravo

AF:

0.146

Asia WGS

AF:

0.0640

AC:

221

AN:

3478

EpiCase

AF:

0.0732

EpiControl

AF:

0.0758

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jul 09, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Genetic Services Laboratory, University of Chicago

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.8

(source)

DANN

Benign

0.76

PhyloP100

0.42

PromoterAI

-0.022

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1834065

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over