rs759134767

chr11-2884860-GGGGGCCGGGGCCGGGGCC-Gchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCGGGGCCGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCchr11-2884860-GGGGGCCGGGGCCGGGGCC-GGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001122630.2(CDKN1C):c.579_596del(p.Ala200_Pro205del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000733 in 1,022,800 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P193P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000049 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000077 (0 hom.)
• Consequence: CDKN1C NM_001122630.2 inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.91

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 11-2884860-GGGGGCCGGGGCCGGGGCC-G is Benign according to our data. Variant chr11-2884860-GGGGGCCGGGGCCGGGGCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 412849.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN1C	NM_001122630.2	c.579_596del	p.Ala200_Pro205del	inframe_deletion	2/4	ENST00000440480.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN1C	ENST00000440480.8	c.579_596del	p.Ala200_Pro205del	inframe_deletion	2/4	1	NM_001122630.2	A2

Frequencies

GnomAD3 genomes AF: 0.0000489 AC: 7 AN: 143230 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000206

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000618

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000773 AC: 68 AN: 879570 Hom.: 0 AF XY: 0.0000842 AC XY: 35 AN XY: 415602

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000114

Gnomad4 FIN exome AF: 0.0000810

Gnomad4 NFE exome AF: 0.0000831

Gnomad4 OTH exome AF: 0.0000312

GnomAD4 genome AF: 0.0000489 AC: 7 AN: 143230 Hom.: 0 Cov.: 32 AF XY: 0.0000717 AC XY: 5 AN XY: 69764

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000206

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000618

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Beckwith-Wiedemann syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759134767; hg19: chr11-2906090;