chr14-91272694-CTT-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001080414.4(CCDC88C):c.6016_6017del(p.Lys2006GlufsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,272 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. K2006K) has been classified as Likely benign.
Frequency
Consequence
NM_001080414.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.6016_6017del | p.Lys2006GlufsTer18 | frameshift_variant | 30/30 | ENST00000389857.11 | |
CCDC88C | XM_011536796.3 | c.5908_5909del | p.Lys1970GlufsTer18 | frameshift_variant | 30/30 | ||
CCDC88C | XM_047431418.1 | c.5749_5750del | p.Lys1917GlufsTer18 | frameshift_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.6016_6017del | p.Lys2006GlufsTer18 | frameshift_variant | 30/30 | 5 | NM_001080414.4 | P1 | |
CCDC88C | ENST00000556726.5 | c.*1850_*1851del | 3_prime_UTR_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459272Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 725976
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Hydrocephalus, nonsyndromic, autosomal recessive 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at