4-786564-C-CTCG
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_006651.4(CPLX1):c.339_341dupCGA(p.Asp113dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,609,724 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006651.4 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPLX1 | ENST00000304062.11 | c.339_341dupCGA | p.Asp113dup | disruptive_inframe_insertion | Exon 4 of 4 | 1 | NM_006651.4 | ENSP00000305613.6 | ||
CPLX1 | ENST00000505203.1 | c.276_278dupCGA | p.Asp92dup | disruptive_inframe_insertion | Exon 5 of 5 | 2 | ENSP00000425960.1 | |||
CPLX1 | ENST00000504062.1 | c.294_296dupCGA | p.Asp98dup | disruptive_inframe_insertion | Exon 3 of 3 | 3 | ENSP00000421947.1 | |||
CPLX1 | ENST00000506404.1 | n.392_394dupCGA | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241472Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131278
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457650Hom.: 0 Cov.: 36 AF XY: 0.00000552 AC XY: 4AN XY: 724830
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.339_341dup, results in the insertion of 1 amino acid(s) of the CPLX1 protein (p.Asp113dup), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with CPLX1-related conditions. This variant is present in population databases (rs746146625, gnomAD 0.002%). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at