11-2884860-GGGGGCCGGGGCCGGGGCCGGGGCCGGGGCT-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001122630.2(CDKN1C):βc.567_596delβ(p.Ala196_Pro205del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000043 in 1,022,798 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β ). Synonymous variant affecting the same amino acid position (i.e. P189P) has been classified as Benign.
Frequency
Consequence
NM_001122630.2 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.567_596del | p.Ala196_Pro205del | inframe_deletion | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.567_596del | p.Ala196_Pro205del | inframe_deletion | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000279 AC: 4AN: 143230Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000455 AC: 40AN: 879568Hom.: 0 AF XY: 0.0000505 AC XY: 21AN XY: 415602
GnomAD4 genome AF: 0.0000279 AC: 4AN: 143230Hom.: 0 Cov.: 32 AF XY: 0.0000430 AC XY: 3AN XY: 69764
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at