1-55039879-ACTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTG
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_174936.4(PCSK9):c.54_65dup(p.Leu20_Leu23dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000456 in 1,557,940 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. P14P) has been classified as Likely benign.
Frequency
Consequence
NM_174936.4 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCSK9 | NM_174936.4 | c.54_65dup | p.Leu20_Leu23dup | inframe_insertion | 1/12 | ENST00000302118.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCSK9 | ENST00000302118.5 | c.54_65dup | p.Leu20_Leu23dup | inframe_insertion | 1/12 | 1 | NM_174936.4 | P2 | |
PCSK9 | ENST00000710286.1 | c.411_422dup | p.Leu139_Leu142dup | inframe_insertion | 1/12 | A2 | |||
PCSK9 | ENST00000673726.1 | c.54_65dup | p.Leu20_Leu23dup | inframe_insertion, NMD_transcript_variant | 1/6 | ||||
PCSK9 | ENST00000673913.2 | c.54_65dup | p.Leu20_Leu23dup | inframe_insertion, NMD_transcript_variant | 1/12 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152070Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000559 AC: 9AN: 161082Hom.: 0 AF XY: 0.0000348 AC XY: 3AN XY: 86248
GnomAD4 exome AF: 0.0000441 AC: 62AN: 1405754Hom.: 0 Cov.: 30 AF XY: 0.0000374 AC XY: 26AN XY: 694300
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74422
ClinVar
Submissions by phenotype
Hypercholesterolemia, autosomal dominant, 3 Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 20, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | This variant, c.54_65dup, results in the insertion of 4 amino acid(s) of the PCSK9 protein (p.Leu20_Leu23dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs371488778, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with PCSK9-related conditions. ClinVar contains an entry for this variant (Variation ID: 662731). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Sep 12, 2022 | The c.54_65dup variant located in exon 1 of this 12-exon gene is predicted to add four Leucine amino acids [p.(Leu20_Leu23dup)] to a stretch of nine consecutive Leucine amino acids without causing a shift in the reading frame (in-frame duplication). This variant has not been previously reported in the literature and is observedin 36 alleles (0.0071% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8) suggesting it is not a common benign variant in the populations represented in those databases. This variant has been deposited in ClinVar [ClinVar ID: 662731] as a Variant of Uncertain Significance (3 entries). In silico predictions are not available for this variant. Based on available evidence, this c.54_65dup p.(Leu20_Leu23dup) variant identified in PCSK9 is classified as a Variant of Uncertain Significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jul 11, 2019 | - - |
Familial hypercholesterolemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Feb 22, 2023 | This variant results in an insertion of four leucine residues in a leucine-rich stretch of the PCSK9 protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with PCSK9-related disorders in the literature. This variant has been identified in 14/192344 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at