6-42929619-TTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006586.5(CNPY3):c.65_76dupTGCTGCTGCTGC(p.Leu22_Leu25dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,950 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000057 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CNPY3
NM_006586.5 disruptive_inframe_insertion
NM_006586.5 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.420
Genes affected
CNPY3 (HGNC:11968): (canopy FGF signaling regulator 3) This gene encodes a protein that binds members of the toll-like receptor protein family and functions as a chaperone to aid in folding and export of these proteins. Alternative splicing results in multiple transcript variants. Naturally occuring readthrough transcription occurs between this locus and the downstream GNMT (glycine N-methyltransferase) gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNPY3 | ENST00000372836.5 | c.65_76dupTGCTGCTGCTGC | p.Leu22_Leu25dup | disruptive_inframe_insertion | Exon 1 of 6 | 1 | NM_006586.5 | ENSP00000361926.4 | ||
ENSG00000287825 | ENST00000667155.3 | n.-152_-141dupGCAGCAGCAGCA | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151950Hom.: 0 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000568 AC: 8AN: 1408520Hom.: 0 Cov.: 31 AF XY: 0.00000575 AC XY: 4AN XY: 696218
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151950Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74200
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at