rs73336474
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001080414.4(CCDC88C):c.3393G>T(p.Ala1131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 1,608,956 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1131A) has been classified as Likely benign.
Frequency
Consequence
NM_001080414.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.3393G>T | p.Ala1131= | synonymous_variant | 20/30 | ENST00000389857.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.3393G>T | p.Ala1131= | synonymous_variant | 20/30 | 5 | NM_001080414.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0177 AC: 2699AN: 152218Hom.: 75 Cov.: 33
GnomAD3 exomes AF: 0.00447 AC: 1095AN: 245204Hom.: 30 AF XY: 0.00329 AC XY: 439AN XY: 133466
GnomAD4 exome AF: 0.00179 AC: 2609AN: 1456622Hom.: 64 Cov.: 33 AF XY: 0.00152 AC XY: 1098AN XY: 724734
GnomAD4 genome AF: 0.0177 AC: 2700AN: 152334Hom.: 75 Cov.: 33 AF XY: 0.0168 AC XY: 1255AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 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 | - - |
CCDC88C-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 19, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at