chr11-27340785-TCTGCTATTTCCTTTTTCTC-T
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_030771.2(CCDC34):c.799_817delGAGAAAAAGGAAATAGCAG(p.Glu267fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
CCDC34
NM_030771.2 frameshift
NM_030771.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.37
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.288 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-27340785-TCTGCTATTTCCTTTTTCTC-T is Pathogenic according to our data. Variant chr11-27340785-TCTGCTATTTCCTTTTTCTC-T is described in ClinVar as [Pathogenic]. Clinvar id is 1710910.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr11-27340785-TCTGCTATTTCCTTTTTCTC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC34 | ENST00000328697.11 | c.799_817delGAGAAAAAGGAAATAGCAG | p.Glu267fs | frameshift_variant | 5/6 | 1 | NM_030771.2 | ENSP00000330240.5 | ||
CCDC34 | ENST00000529615.1 | n.286_304delGAGAAAAAGGAAATAGCAG | non_coding_transcript_exon_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Spermatogenic failure 76 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 17, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.