rs199536020
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001080414.4(CCDC88C):c.3900C>T(p.Phe1300=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000342 in 1,613,592 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0013 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00024 ( 2 hom. )
Consequence
CCDC88C
NM_001080414.4 synonymous
NM_001080414.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.406
Genes affected
CCDC88C (HGNC:19967): (coiled-coil domain containing 88C) This gene encodes a ubiquitously expressed coiled-coil domain-containing protein that interacts with the dishevelled protein and is a negative regulator of the Wnt signalling pathway. The protein encoded by this gene has a PDZ-domain binding motif in its C-terminus with which it interacts with the dishevelled protein. Dishevelled is a scaffold protein involved in the regulation of the Wnt signaling pathway. The Wnt signaling pathway plays an important role in embryonic development, tissue maintenance, and cancer progression. Mutations in this gene cause autosomal recessive, primary non-syndromic congenital hydrocephalus; a condition characterized by excessive accumulation of cerebrospinal fluid in the ventricles of the brain. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 14-91297371-G-A is Benign according to our data. Variant chr14-91297371-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 447016.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-91297371-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.406 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00128 (195/152336) while in subpopulation AFR AF= 0.00445 (185/41586). AF 95% confidence interval is 0.00392. There are 1 homozygotes in gnomad4. There are 95 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.3900C>T | p.Phe1300= | synonymous_variant | 22/30 | ENST00000389857.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.3900C>T | p.Phe1300= | synonymous_variant | 22/30 | 5 | NM_001080414.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 195AN: 152218Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000565 AC: 140AN: 247970Hom.: 0 AF XY: 0.000498 AC XY: 67AN XY: 134626
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GnomAD4 exome AF: 0.000244 AC: 357AN: 1461256Hom.: 2 Cov.: 33 AF XY: 0.000245 AC XY: 178AN XY: 726830
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GnomAD4 genome ? AF: 0.00128 AC: 195AN: 152336Hom.: 1 Cov.: 33 AF XY: 0.00128 AC XY: 95AN XY: 74486
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at