chr6-53006372-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014920.5(CILK1):c.1687G>T(p.Glu563*) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000684 in 1,461,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_014920.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CILK1 | NM_014920.5 | c.1687G>T | p.Glu563* | stop_gained | Exon 13 of 14 | ENST00000676107.1 | NP_055735.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CILK1 | ENST00000676107.1 | c.1687G>T | p.Glu563* | stop_gained | Exon 13 of 14 | NM_014920.5 | ENSP00000501692.1 | |||
CILK1 | ENST00000350082.10 | c.1708G>T | p.Glu570* | stop_gained | Exon 13 of 14 | 1 | ENSP00000263043.8 | |||
CILK1 | ENST00000356971.3 | c.1687G>T | p.Glu563* | stop_gained | Exon 14 of 15 | 2 | ENSP00000349458.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251386Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135862
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461682Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727158
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: CILK1 c.1687G>T (p.Glu563X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, however current evidence is not sufficient to establish loss-of-function variants in CILK1 as causative of disease. The variant allele was found at a frequency of 4e-06 in 251386 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1687G>T in individuals affected with CILK1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 500316). Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at