11-2884890-TGGGGCC-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001122630.2(CDKN1C):c.561_566del(p.Ala204_Pro205del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 741,354 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P187P) 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.561_566del | p.Ala204_Pro205del | inframe_deletion | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.561_566del | p.Ala204_Pro205del | inframe_deletion | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000928 AC: 1AN: 107750Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000221 AC: 14AN: 633604Hom.: 0 AF XY: 0.0000168 AC XY: 5AN XY: 298166
GnomAD4 genome AF: 0.00000928 AC: 1AN: 107750Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 52988
ClinVar
Submissions by phenotype
CDKN1C-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 08, 2023 | The CDKN1C c.594_599del6 variant is predicted to result in an in-frame deletion (p.Ala215_Pro216del). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Beckwith-Wiedemann syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at