Variant chr16-88805500-A-G 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.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

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:

CDT1 (HGNC:):

CDT1 links:

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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=-0.59).

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. Variant chr16-88805500-A-G is described in Lovd as [Benign].

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/exons	MANE	Protein	UniProt
CDT1	NM_030928.4 linkuse as main transcript	c.549A>G	p.Gly183Gly	synonymous_variant	4/10	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.549A>G	p.Gly183Gly	synonymous_variant	4/10	1	NM_030928.4	ENSP00000301019.4		Q9H211
CDT1	ENST00000562747.1 linkuse as main transcript	n.255A>G		non_coding_transcript_exon_variant	3/5	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

GnomAD3 exomes

AF:

0.0837

AC:

20894

AN:

249580

Hom.:

1590

AF XY:

0.0828

AC XY:

11221

AN XY:

135550

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 SAS exome

AF:

0.121

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

Gnomad4 AFR exome

AF:

0.322

Gnomad4 AMR exome

AF:

0.0573

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.00237

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.0218

Gnomad4 NFE exome

AF:

0.0632

Gnomad4 OTH exome

AF:

0.0848

GnomAD4 genome

AF:

0.134

AC:

20339

AN:

152172

Hom.:

2318

Cov.:

AF XY:

0.130

AC XY:

9681

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.310

Gnomad4 AMR

AF:

0.0821

Gnomad4 ASJ

AF:

0.168

Gnomad4 EAS

AF:

0.00329

Gnomad4 SAS

AF:

0.110

Gnomad4 FIN

AF:

0.0197

Gnomad4 NFE

AF:

0.0665

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.0947

Hom.:

1216

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
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	- -

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

-0.59

CADD

Benign

6.8

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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