11-2884917-GGCCGGAGCCGGAGCCGGA-GGCCGGA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001122630.2(CDKN1C):c.528_539delTCCGGCTCCGGC(p.Pro177_Ala180del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000102 in 882,232 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
CDKN1C
NM_001122630.2 disruptive_inframe_deletion
NM_001122630.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.216
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 11-2884917-GGCCGGAGCCGGA-G is Benign according to our data. Variant chr11-2884917-GGCCGGAGCCGGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1141196.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000695 AC: 1AN: 143804Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000108 AC: 8AN: 738428Hom.: 0 AF XY: 0.00000861 AC XY: 3AN XY: 348426
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GnomAD4 genome AF: 0.00000695 AC: 1AN: 143804Hom.: 0 Cov.: 32 AF XY: 0.0000143 AC XY: 1AN XY: 69918
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Beckwith-Wiedemann syndrome Benign:1
Sep 08, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at