chr11-2884908-T-C
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001122630.2(CDKN1C):āc.549A>Gā(p.Pro183=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P183P) has been classified as Likely benign.
Frequency
Genomes: š 0.000017 ( 0 hom., cov: 32)
Exomes š: 0.0000031 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CDKN1C
NM_001122630.2 synonymous
NM_001122630.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.192
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 -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 11-2884908-T-C is Benign according to our data. Variant chr11-2884908-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 454016.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.192 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.549A>G | p.Pro183= | synonymous_variant | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.549A>G | p.Pro183= | synonymous_variant | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 116964Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome AF: 0.00000306 AC: 2AN: 653046Hom.: 0 Cov.: 9 AF XY: 0.00000325 AC XY: 1AN XY: 308002
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000171 AC: 2AN: 116964Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 57200
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Data not reliable, filtered out with message: AS_VQSR
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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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at