17-40289585-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001254.4(CDC6):​c.165C>T​(p.Pro55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,613,974 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0012 ( 3 hom., cov: 31)
Exomes 𝑓: 0.0016 ( 12 hom. )

Consequence

CDC6
NM_001254.4 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.208
Variant links:
Genes affected
CDC6 (HGNC:1744): (cell division cycle 6) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Cdc6, a protein essential for the initiation of DNA replication. This protein functions as a regulator at the early steps of DNA replication. It localizes in cell nucleus during cell cyle G1, but translocates to the cytoplasm at the start of S phase. The subcellular translocation of this protein during cell cyle is regulated through its phosphorylation by Cdks. Transcription of this protein was reported to be regulated in response to mitogenic signals through transcriptional control mechanism involving E2F proteins. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BP6
Variant 17-40289585-C-T is Benign according to our data. Variant chr17-40289585-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 210619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-40289585-C-T is described in Lovd as [Benign]. Variant chr17-40289585-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.208 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0016 (2339/1461724) while in subpopulation MID AF= 0.0199 (115/5768). AF 95% confidence interval is 0.017. There are 12 homozygotes in gnomad4_exome. There are 1330 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDC6NM_001254.4 linkuse as main transcriptc.165C>T p.Pro55= synonymous_variant 2/12 ENST00000209728.9 NP_001245.1
CDC6XM_011525541.3 linkuse as main transcriptc.165C>T p.Pro55= synonymous_variant 2/13 XP_011523843.1
CDC6XM_011525542.2 linkuse as main transcriptc.165C>T p.Pro55= synonymous_variant 2/13 XP_011523844.1
CDC6XM_047437207.1 linkuse as main transcriptc.165C>T p.Pro55= synonymous_variant 2/12 XP_047293163.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDC6ENST00000209728.9 linkuse as main transcriptc.165C>T p.Pro55= synonymous_variant 2/121 NM_001254.4 ENSP00000209728 P1

Frequencies

GnomAD3 genomes
AF:
0.00123
AC:
187
AN:
152132
Hom.:
3
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000290
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.00131
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00497
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00148
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00221
AC:
556
AN:
251396
Hom.:
3
AF XY:
0.00252
AC XY:
342
AN XY:
135890
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00147
Gnomad ASJ exome
AF:
0.00536
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00653
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.00200
Gnomad OTH exome
AF:
0.00342
GnomAD4 exome
AF:
0.00160
AC:
2339
AN:
1461724
Hom.:
12
Cov.:
31
AF XY:
0.00183
AC XY:
1330
AN XY:
727170
show subpopulations
Gnomad4 AFR exome
AF:
0.000359
Gnomad4 AMR exome
AF:
0.00152
Gnomad4 ASJ exome
AF:
0.00455
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00646
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.00120
Gnomad4 OTH exome
AF:
0.00205
GnomAD4 genome
AF:
0.00122
AC:
185
AN:
152250
Hom.:
3
Cov.:
31
AF XY:
0.00121
AC XY:
90
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.000289
Gnomad4 AMR
AF:
0.00131
Gnomad4 ASJ
AF:
0.00346
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00477
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00148
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00181
Hom.:
1
Bravo
AF:
0.00127
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.00229
EpiControl
AF:
0.00284

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:4
Likely benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 23, 2024- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2024CDC6: BP4, BP7, BS2 -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
not specified Benign:3
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Likely benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoAug 06, 2015- -
Benign, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Meier-Gorlin syndrome 5 Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
CADD
Benign
12
DANN
Benign
0.75
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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.

Other links and lift over

dbSNP: rs142289528; hg19: chr17-38445837; API