15-40562852-T-TCC
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001080792.4(CCDC32):c.163_164insGG(p.Glu55GlyfsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
CCDC32
NM_001080792.4 frameshift
NM_001080792.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.05
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-40562852-T-TCC is Pathogenic according to our data. Variant chr15-40562852-T-TCC is described in ClinVar as [Pathogenic]. Clinvar id is 988601.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC32 | NM_001080792.4 | c.163_164insGG | p.Glu55GlyfsTer12 | frameshift_variant | 2/4 | ENST00000416810.7 | NP_001074261.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC32 | ENST00000416810.7 | c.163_164insGG | p.Glu55GlyfsTer12 | frameshift_variant | 2/4 | 1 | NM_001080792.4 | ENSP00000397515 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cardiofacioneurodevelopmental syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 09, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at