rs183742506
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001080414.4(CCDC88C):c.766C>T(p.Leu256=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00351 in 1,613,598 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L256L) 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 -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.766C>T | p.Leu256= | synonymous_variant | 8/30 | ENST00000389857.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.766C>T | p.Leu256= | synonymous_variant | 8/30 | 5 | NM_001080414.4 | P1 | |
CCDC88C | ENST00000554872.5 | n.706C>T | non_coding_transcript_exon_variant | 7/7 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00271 AC: 412AN: 152252Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00246 AC: 609AN: 247742Hom.: 3 AF XY: 0.00241 AC XY: 325AN XY: 134662
GnomAD4 exome AF: 0.00359 AC: 5253AN: 1461228Hom.: 13 Cov.: 31 AF XY: 0.00349 AC XY: 2535AN XY: 726894
GnomAD4 genome AF: 0.00270 AC: 412AN: 152370Hom.: 1 Cov.: 33 AF XY: 0.00251 AC XY: 187AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CCDC88C: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 22, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at