rs878853627
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2
The NM_001122630.2(CDKN1C):c.461_466del(p.Val154_Ala155del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,104,384 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. V154V) has been classified as Likely benign.
Frequency
Consequence
NM_001122630.2 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.461_466del | p.Val154_Ala155del | inframe_deletion | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.461_466del | p.Val154_Ala155del | inframe_deletion | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000549 AC: 8AN: 145644Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.000117 AC: 112AN: 958628Hom.: 0 AF XY: 0.000103 AC XY: 47AN XY: 456714
GnomAD4 genome ? AF: 0.0000549 AC: 8AN: 145756Hom.: 0 Cov.: 30 AF XY: 0.0000421 AC XY: 3AN XY: 71260
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | CDKN1C: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at