Sequencing platform: Illumina.db
In this step the following thresholds are used:
The table contains all HPO and/or suspected diseases considered when ranking the variants.
| Patient ID | Term | Description |
|---|---|---|
| SNG190 | HP:0000098 | Tall stature |
| SNG190 | HP:0000202 | Oral cleft |
| SNG190 | HP:0000316 | Hypertelorism |
| SNG190 | HP:0000337 | Broad forehead |
| SNG190 | HP:0002107 | Pneumothorax |
| SNG190 | HP:0002664 | Neoplasm |
| SNG190 | HP:0002744 | Bilateral cleft lip and palate |
| SNG190 | HP:0100336 | Bilateral cleft lip |
The table is sorted by variants in genes associated with the patient’s disease phenotype and then by descending CADD score. In addition, all variants occuring in more than 5 patients are given a low priority. Variants with a call quality of less than 10 are discarded.
Legend:
| Column | Description |
|---|---|
| Rank | rank of variant after sorting the list according to the criteria above |
| pos | genomic coordinates |
| GTS | genotype |
| PhenolyzerScore | contains a score for genes returned by phenolyzer |
| OMIMAPI | contain genes associated with the patients disease phenotype |
| CallQ | Phred scaled call quality |
| Depth | Read depth |
| RefD | Depth of reference allele |
| AltD | Depth of alternate allele |
| cadd_scaled | Scaled CADD score - NOTE: for visualization purposes all indels are given a score of 15.555 and blue cell color. |
| pvs1 | null variant in a gene where LOF is a known mechanism of disease | pvs1_caution | Is the variant in the last exon? |
| ps1 | Same amino acid change as a previously established pathogenic variant regardless of nucleotide change | ps1_caution | If ps1 = 1, shows codon change |
| pm1 | Located in a mutational hot spot and/or critical and well-established functional domain without benign variation | pm1_caution | Always empty |
| pm2 | Absent from controls (or at extremely low frequency if recessive) | pm2_caution | Always empty |
| pm4 | Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants | pm4_caution | Always empty |
| pm5 | Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before | pm5_caution | If pm5 = 1, shows known allele change |
| pp2 | Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease | pp2_caution | Shows connection errors if any |
| pp3 | Multiple lines of computational evidence support a deleterious effect on the gene or gene product | pp3_caution | Shows number of computational tools (n=3) displaying significant scores |