rs201222692
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001080414.4(CCDC88C):āc.4433T>Cā(p.Val1478Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000977 in 1,611,524 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001080414.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.4433T>C | p.Val1478Ala | missense_variant | 25/30 | ENST00000389857.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.4433T>C | p.Val1478Ala | missense_variant | 25/30 | 5 | NM_001080414.4 | P1 | |
CCDC88C | ENST00000556726.5 | c.221T>C | p.Val74Ala | missense_variant | 1/7 | 5 | |||
CCDC88C | ENST00000555995.1 | n.308T>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00569 AC: 863AN: 151632Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00143 AC: 351AN: 244756Hom.: 4 AF XY: 0.00104 AC XY: 138AN XY: 133290
GnomAD4 exome AF: 0.000486 AC: 710AN: 1459774Hom.: 4 Cov.: 31 AF XY: 0.000424 AC XY: 308AN XY: 726256
GnomAD4 genome ? AF: 0.00570 AC: 865AN: 151750Hom.: 8 Cov.: 32 AF XY: 0.00561 AC XY: 416AN XY: 74162
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 20, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Hydrocephalus, nonsyndromic, autosomal recessive 1;C4518336:Spinocerebellar ataxia type 40 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at