Variant 11-2883974-GC-GCCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001122630.2(CDKN1C):c.*5+23_*5+24dupGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0037 in 1,553,992 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0038 ( 10 hom. )

Consequence

CDKN1C
NM_001122630.2 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

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]

CDKN1C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-2883974-G-GCC is Benign according to our data. Variant chr11-2883974-G-GCC is described in ClinVar as [Likely_benign]. Clinvar id is 2641505.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00288 (437/151700) while in subpopulation AMR AF= 0.00484 (74/15278). AF 95% confidence interval is 0.00396. There are 0 homozygotes in gnomad4. There are 221 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High AC in GnomAd4 at 437 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKN1C	NM_001122630.2 link	c.5+23_5+24dupGG		intron_variant	Intron 3 of 3	ENST00000440480.8	NP_001116102.1	P49918-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKN1C	ENST00000440480.8 link	c.5+24_5+25insGG		intron_variant	Intron 3 of 3	1	NM_001122630.2	ENSP00000411257.2		P49918-2

Frequencies

GnomAD3 genomes

AF:

0.00289

AC:

438

AN:

151584

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000992

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00492

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000392

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00562

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00355

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00287

AC:

448

AN:

155866

Hom.:

AF XY:

0.00279

AC XY:

238

AN XY:

85418

show subpopulations

Gnomad AFR exome

AF:

0.000650

Gnomad AMR exome

AF:

0.00356

Gnomad ASJ exome

AF:

0.00336

Gnomad EAS exome

AF:

0.000695

Gnomad SAS exome

AF:

0.00115

Gnomad FIN exome

AF:

0.00469

Gnomad NFE exome

AF:

0.00358

Gnomad OTH exome

AF:

0.00138

GnomAD4 exome

AF:

0.00378

AC:

5306

AN:

1402292

Hom.:

Cov.:

AF XY:

0.00372

AC XY:

2578

AN XY:

692672

show subpopulations

Gnomad4 AFR exome

AF:

0.000868

Gnomad4 AMR exome

AF:

0.00348

Gnomad4 ASJ exome

AF:

0.00330

Gnomad4 EAS exome

AF:

0.000494

Gnomad4 SAS exome

AF:

0.00128

Gnomad4 FIN exome

AF:

0.00472

Gnomad4 NFE exome

AF:

0.00423

Gnomad4 OTH exome

AF:

0.00248

GnomAD4 genome

AF:

0.00288

AC:

437

AN:

151700

Hom.:

Cov.:

AF XY:

0.00298

AC XY:

221

AN XY:

74142

show subpopulations

Gnomad4 AFR

AF:

0.000989

Gnomad4 AMR

AF:

0.00484

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.000393

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00562

Gnomad4 NFE

AF:

0.00355

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.00169

Hom.:

952

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CDKN1C: BS1 -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over