rs45542736
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001080414.4(CCDC88C):āc.5948G>Cā(p.Gly1983Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 1,607,908 control chromosomes in the GnomAD database, including 342 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as 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.5948G>C | p.Gly1983Ala | missense_variant | 30/30 | ENST00000389857.11 | |
CCDC88C | XM_011536796.3 | c.5840G>C | p.Gly1947Ala | missense_variant | 30/30 | ||
CCDC88C | XM_047431418.1 | c.5681G>C | p.Gly1894Ala | missense_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.5948G>C | p.Gly1983Ala | missense_variant | 30/30 | 5 | NM_001080414.4 | P1 | |
CCDC88C | ENST00000556726.5 | c.*1782G>C | 3_prime_UTR_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0154 AC: 2340AN: 152216Hom.: 39 Cov.: 32
GnomAD3 exomes AF: 0.0189 AC: 4534AN: 240012Hom.: 96 AF XY: 0.0198 AC XY: 2606AN XY: 131408
GnomAD4 exome AF: 0.0172 AC: 25079AN: 1455574Hom.: 303 Cov.: 34 AF XY: 0.0174 AC XY: 12579AN XY: 723968
GnomAD4 genome ? AF: 0.0153 AC: 2337AN: 152334Hom.: 39 Cov.: 32 AF XY: 0.0178 AC XY: 1326AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 08, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at