rs1159599818
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001122630.2(CDKN1C):c.414_431del(p.Val140_Pro145del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000071 in 1,267,460 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. P138P) 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.414_431del | p.Val140_Pro145del | inframe_deletion | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.414_431del | p.Val140_Pro145del | inframe_deletion | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000696 AC: 1AN: 143774Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000712 AC: 8AN: 1123686Hom.: 0 AF XY: 0.00000370 AC XY: 2AN XY: 540924
GnomAD4 genome ? AF: 0.00000696 AC: 1AN: 143774Hom.: 0 Cov.: 33 AF XY: 0.0000142 AC XY: 1AN XY: 70194
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at