chr6-42929619-T-TTGCTGCTGCTGCTGC
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006586.5(CNPY3):c.62_76dup(p.Leu21_Leu25dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,950 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000050 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CNPY3
NM_006586.5 inframe_insertion
NM_006586.5 inframe_insertion
Scores
Not classified
Clinical Significance
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNPY3 | NM_006586.5 | c.62_76dup | p.Leu21_Leu25dup | inframe_insertion | 1/6 | ENST00000372836.5 | |
CNPY3-GNMT | NR_134890.2 | n.153_167dup | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNPY3 | ENST00000372836.5 | c.62_76dup | p.Leu21_Leu25dup | inframe_insertion | 1/6 | 1 | NM_006586.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000497 AC: 7AN: 1408520Hom.: 0 Cov.: 31 AF XY: 0.00000575 AC XY: 4AN XY: 696218
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74200
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy, 60 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Jul 08, 2024 | The variant c.62_76dup (p.L21_L25dup) was detected homozygous in CNPY3 gene. The variant has not been reported for its pathogenicity in ClinVar. The frequency of it in public population databases is very low. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at