11-2884917-GGCCGGAGCCGGAGCCGGA-GGCCGGAGCCGGA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001122630.2(CDKN1C):​c.534_539delTCCGGC​(p.Pro179_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 0.000436 in 882,284 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 0 hom. )

Consequence

CDKN1C
NM_001122630.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:4

Conservation

PhyloP100: 0.0360
Variant links:
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 -9 ACMG points.

BP6
Variant 11-2884917-GGCCGGA-G is Benign according to our data. Variant chr11-2884917-GGCCGGA-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 236958.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1, Likely_benign=2}.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000723 (104/143898) while in subpopulation SAS AF= 0.00211 (10/4744). AF 95% confidence interval is 0.00147. There are 0 homozygotes in gnomad4. There are 53 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 104 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDKN1CNM_001122630.2 linkc.534_539delTCCGGC p.Pro179_Ala180del disruptive_inframe_deletion Exon 2 of 4 ENST00000440480.8 NP_001116102.1 P49918-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDKN1CENST00000440480.8 linkc.534_539delTCCGGC p.Pro179_Ala180del disruptive_inframe_deletion Exon 2 of 4 1 NM_001122630.2 ENSP00000411257.2 P49918-2

Frequencies

GnomAD3 genomes
AF:
0.000723
AC:
104
AN:
143802
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000957
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00204
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00179
Gnomad SAS
AF:
0.00211
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000275
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000381
AC:
281
AN:
738386
Hom.:
0
AF XY:
0.000390
AC XY:
136
AN XY:
348408
show subpopulations
Gnomad4 AFR exome
AF:
0.000783
Gnomad4 AMR exome
AF:
0.000313
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000523
Gnomad4 SAS exome
AF:
0.00130
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000353
Gnomad4 OTH exome
AF:
0.000569
GnomAD4 genome
AF:
0.000723
AC:
104
AN:
143898
Hom.:
0
Cov.:
32
AF XY:
0.000757
AC XY:
53
AN XY:
70026
show subpopulations
Gnomad4 AFR
AF:
0.000954
Gnomad4 AMR
AF:
0.00204
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00179
Gnomad4 SAS
AF:
0.00211
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000275
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:4
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024CDKN1C: BS1 -
Uncertain significance, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Jun 10, 2015- -
CDKN1C-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesOct 07, 2020This 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). -
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsMay 26, 2021This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Beckwith-Wiedemann syndrome Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 14, 2025- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs878853632; hg19: chr11-2906147; API