rs112741231
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001080414.4(CCDC88C):c.3372G>A(p.Thr1124=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00429 in 1,602,506 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 104 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 88 hom. )
Consequence
CCDC88C
NM_001080414.4 synonymous
NM_001080414.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.84
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=-0.73).
BP6
?
Variant 14-91303964-C-T is Benign according to our data. Variant chr14-91303964-C-T is described in ClinVar as [Benign]. Clinvar id is 158107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-4.84 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.065 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.3372G>A | p.Thr1124= | synonymous_variant | 20/30 | ENST00000389857.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.3372G>A | p.Thr1124= | synonymous_variant | 20/30 | 5 | NM_001080414.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0200 AC: 3046AN: 152220Hom.: 98 Cov.: 33
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GnomAD3 exomes AF: 0.00569 AC: 1376AN: 241776Hom.: 37 AF XY: 0.00434 AC XY: 573AN XY: 131924
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GnomAD4 exome AF: 0.00262 AC: 3801AN: 1450168Hom.: 88 Cov.: 33 AF XY: 0.00238 AC XY: 1712AN XY: 720808
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GnomAD4 genome ? AF: 0.0202 AC: 3072AN: 152338Hom.: 104 Cov.: 33 AF XY: 0.0196 AC XY: 1461AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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