11-2884923-AGCCGGAGCCGGAGCCGGGGCCGGG-AGCCGGAGCCGGAGCCGGGGCCGGGGCCGGAGCCGGAGCCGGGGCCGGG
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001122630.2(CDKN1C):c.533_534insCCCGGCCCCGGCTCCGGCTCCGGC(p.Ala176_Pro183dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A178A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CDKN1C
NM_001122630.2 inframe_insertion
NM_001122630.2 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.731
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 11-2884923-A-AGCCGGAGCCGGAGCCGGGGCCGGG is Benign according to our data. Variant chr11-2884923-A-AGCCGGAGCCGGAGCCGGGGCCGGG is described in ClinVar as [Likely_benign]. Clinvar id is 743884.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.533_534insCCCGGCCCCGGCTCCGGCTCCGGC | p.Ala176_Pro183dup | inframe_insertion | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.533_534insCCCGGCCCCGGCTCCGGCTCCGGC | p.Ala176_Pro183dup | inframe_insertion | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 687316Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0AN XY: 325552
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
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0
AN:
687316
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Cov.:
11
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AC XY:
0
AN XY:
325552
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Beckwith-Wiedemann syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2022 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at