NM_006586.5:c.62_76dupTGCTGCTGCTGCTGC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006586.5(CNPY3):c.62_76dupTGCTGCTGCTGCTGC(p.Leu21_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 0.00000658 in 151,950 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006586.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNPY3 | ENST00000372836.5 | c.62_76dupTGCTGCTGCTGCTGC | p.Leu21_Leu25dup | disruptive_inframe_insertion | Exon 1 of 6 | 1 | NM_006586.5 | ENSP00000361926.4 | ||
ENSG00000287825 | ENST00000667155.3 | n.-155_-141dupGCAGCAGCAGCAGCA | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 33
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
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151950Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74200
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 60 Uncertain:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at