rs565544512
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The ENST00000440480.8(CDKN1C):βc.467_490delβ(p.Ala156_Ala163del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 981,980 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β ).
Frequency
Genomes: π 0.000022 ( 0 hom., cov: 25)
Exomes π: 0.000022 ( 0 hom. )
Consequence
CDKN1C
ENST00000440480.8 inframe_deletion
ENST00000440480.8 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.593
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 11-2884966-ACCGCGACCGGAGCCGCGACCGGAG-A is Benign according to our data. Variant chr11-2884966-ACCGCGACCGGAGCCGCGACCGGAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 454006.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.467_490del | p.Ala156_Ala163del | inframe_deletion | 2/4 | ENST00000440480.8 | NP_001116102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.467_490del | p.Ala156_Ala163del | inframe_deletion | 2/4 | 1 | NM_001122630.2 | ENSP00000411257 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000220 AC: 3AN: 136442Hom.: 0 Cov.: 25
GnomAD3 genomes
AF:
AC:
3
AN:
136442
Hom.:
Cov.:
25
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000225 AC: 19AN: 845538Hom.: 0 AF XY: 0.0000173 AC XY: 7AN XY: 404056
GnomAD4 exome
AF:
AC:
19
AN:
845538
Hom.:
AF XY:
AC XY:
7
AN XY:
404056
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000220 AC: 3AN: 136442Hom.: 0 Cov.: 25 AF XY: 0.0000302 AC XY: 2AN XY: 66298
GnomAD4 genome
AF:
AC:
3
AN:
136442
Hom.:
Cov.:
25
AF XY:
AC XY:
2
AN XY:
66298
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 02, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at