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
NM_001122630.2 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.198
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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000244 AC: 33AN: 135124Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000418 AC: 1AN: 23948Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 15782
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GnomAD4 exome AF: 0.000102 AC: 101AN: 994090Hom.: 0 Cov.: 22 AF XY: 0.000116 AC XY: 55AN XY: 475940
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GnomAD4 genome AF: 0.000244 AC: 33AN: 135222Hom.: 0 Cov.: 33 AF XY: 0.000288 AC XY: 19AN XY: 65872
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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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2025 | - - |
Pathogenic, no assertion criteria provided | not provided | Centre de Recherche Saint Antoine, Université Pierre et Marie Curie | - | - - |
CDKN1C-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 21, 2024 | This 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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | CDKN1C: BS1 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at