11-2884917-GGCCGGAGCCGGAGCCGGA-GGCCGGAGCCGGAGCCGGAGCCGGA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001122630.2(CDKN1C):c.534_539dupTCCGGC(p.Ala180_Pro181insProAla) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000034 in 882,332 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
CDKN1C
NM_001122630.2 disruptive_inframe_insertion
NM_001122630.2 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.823
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 -10 ACMG points.
BP6
Variant 11-2884917-G-GGCCGGA is Benign according to our data. Variant chr11-2884917-G-GGCCGGA is described in ClinVar as [Likely_benign]. Clinvar id is 454014.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0000417 (6/143900) while in subpopulation AFR AF= 0.000103 (4/38792). AF 95% confidence interval is 0.000035. There are 0 homozygotes in gnomad4. There are 5 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000417 AC: 6AN: 143804Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000325 AC: 24AN: 738432Hom.: 0 Cov.: 10 AF XY: 0.0000488 AC XY: 17AN XY: 348430
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GnomAD4 genome AF: 0.0000417 AC: 6AN: 143900Hom.: 0 Cov.: 32 AF XY: 0.0000714 AC XY: 5AN XY: 70028
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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
Dec 16, 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