11-2884840-TCCGGGGCCGGGGCCGGGG-TCCGGGGCCGGGGCCGGGGCCGGGG

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001122630.2(CDKN1C):​c.611_616dupCCCCGG​(p.Ala204_Pro205dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,129,312 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 0 hom. )

Consequence

CDKN1C
NM_001122630.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts P:1B:3

Conservation

PhyloP100: -0.198
Variant links:
Genes affected
CDKN1C (HGNC:1786): (cyclin dependent kinase inhibitor 1C) This gene is imprinted, with preferential expression of the maternal allele. The encoded protein is a tight-binding, strong inhibitor of several G1 cyclin/Cdk complexes and a negative regulator of cell proliferation. Mutations in this gene are implicated in sporadic cancers and Beckwith-Wiedemann syndorome, suggesting that this gene is a tumor suppressor candidate. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6
Variant 11-2884840-T-TCCGGGG is Benign according to our data. Variant chr11-2884840-T-TCCGGGG is described in ClinVar as [Likely_benign]. Clinvar id is 192358.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000244 (33/135222) while in subpopulation SAS AF= 0.00202 (8/3964). AF 95% confidence interval is 0.001. There are 0 homozygotes in gnomad4. There are 19 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 33 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDKN1CNM_001122630.2 linkc.611_616dupCCCCGG p.Ala204_Pro205dup conservative_inframe_insertion Exon 2 of 4 ENST00000440480.8 NP_001116102.1 P49918-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDKN1CENST00000440480.8 linkc.611_616dupCCCCGG p.Ala204_Pro205dup conservative_inframe_insertion Exon 2 of 4 1 NM_001122630.2 ENSP00000411257.2 P49918-2

Frequencies

GnomAD3 genomes
AF:
0.000244
AC:
33
AN:
135124
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000110
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000722
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00202
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000317
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000418
AC:
1
AN:
23948
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
15782
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000860
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000102
AC:
101
AN:
994090
Hom.:
0
Cov.:
22
AF XY:
0.000116
AC XY:
55
AN XY:
475940
show subpopulations
Gnomad4 AFR exome
AF:
0.000104
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000225
Gnomad4 SAS exome
AF:
0.00107
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000678
Gnomad4 OTH exome
AF:
0.000137
GnomAD4 genome
AF:
0.000244
AC:
33
AN:
135222
Hom.:
0
Cov.:
33
AF XY:
0.000288
AC XY:
19
AN XY:
65872
show subpopulations
Gnomad4 AFR
AF:
0.000110
Gnomad4 AMR
AF:
0.0000722
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00202
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000317
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Likely benign
Submissions summary: Pathogenic:1Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Beckwith-Wiedemann syndrome Pathogenic:1Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 23, 2025- -
Pathogenic, no assertion criteria providednot providedCentre de Recherche Saint Antoine, Université Pierre et Marie Curie-- -
CDKN1C-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 21, 2024This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMay 01, 2023CDKN1C: BS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs772704243; hg19: chr11-2906070; API