chr11-27340785-TCTGCTATTTCCTTTTTCTC-T

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

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 7.37
Variant links:
Genes affected
CCDC34 (HGNC:25079): (coiled-coil domain containing 34)

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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

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC34NM_030771.2 linkc.799_817delGAGAAAAAGGAAATAGCAG p.Glu267fs frameshift_variant 5/6 ENST00000328697.11 NP_110398.1 Q96HJ3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC34ENST00000328697.11 linkc.799_817delGAGAAAAAGGAAATAGCAG p.Glu267fs frameshift_variant 5/61 NM_030771.2 ENSP00000330240.5 Q96HJ3-1
CCDC34ENST00000529615.1 linkn.286_304delGAGAAAAAGGAAATAGCAG non_coding_transcript_exon_variant 3/63

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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 providedliterature onlyOMIMOct 17, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-27362332; API