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        "author": "bars",
        "author_email": "barslmn@gmail.com",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Topic :: Software Development :: Build Tools"
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        "description": "# Picus\nPointed Interpretation of Clinical Variant Significance\n\n## Quick Install\n* Linux&Mac\n\n> sudo pip3 install picus\n\n* Windows\n\n> pip install picus\n\n## Example Uses\n\n* Picus examples\n\n> picus -i input.csv -o output.json\n\n\n## Evidence Collection Process\n\n### PVS1\n* PVS1 null variant (nonsense, frameshift, canonical \u00b11 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease.\n\n#### Status\n* Implemented\n\n#### Resources\n* LoF genes list from intervar. https://raw.githubusercontent.com/barslmn/InterVar/master/intervardb/PVS1.LOF.genes.hg19\n* Null variants defined as HIGH IMPACT by https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html\n\n#### Conditions\n* \"gene_symbol\" is in LoF gene list.\n* \"transcript_consequence_terms\" is high impact.\n\n#### Shortcomings\n* LoF gene list is only predictive and may be missing some actual LoF genes.\n* No checks for multiexon deletion.\n\n### PS1\n* Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.\n\n#### Status\n* Implemented\n\n#### Resources\n* Clinvar xml (ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/)\n\n#### Annotation Steps\n1. Clinvar data is parsed using https://github.com/barslmn/clinvar.\n2. Sample data and clinvar data is merged based on columns \"CHR\" and \"POS\".\n3. Clinvar feature columns \"ALT\", \"hgvsp\", and \"clinical_significance\" added to original annotation.\n\n#### Conditions\n1. \"clinical_significance\" is pathogenic.\n2. Sample \"hgvsp\" and later added clinvar \"hgvsp\" changes are the same.\n3. Sample \"ALT\" and clinvar \"ALT\" are different.\n\n#### Shortcomings\n\n### PS2\n* De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.\n\n#### Status\n* Not Checked\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PS3\n* Well-established\u2002in\u2002vitro\u2002or\u2002in\u2002vivo\u2002functional\u2002studies\u2002supportive\u2002of\u2002a\u2002damaging\u2002effect\u2002on\u2002the\u2002gene\u2002or\u2002gene\u2002product\n\n#### Status\n* Not Checked\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PS4\n* The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls\n\n#### Status\n* Implemented\n\n#### Resources\n* Intervar\n\n#### Conditions\n1. \"id\" is in id list.\n\n#### Shortcomings\n1. No idea how the source is made.\n\n### PM1\n* Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation\n\n#### Status\n* Planned.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PM2\n* Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium\n\n#### Status\n* Implemented\n\n#### Resources\n* VEP\n\n#### Conditions\n* \"gnomad\" less than 0.001.\n\n#### Shortcomings\n\n### PM3\n* For\u2002recessive\u2002disorders,\u2002detected\u2002in\u2002trans with a pathogenic variant\n\n#### Status\n* Planned for trio\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PM4\n* Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants\n\n#### Status\n* Implemented\n\n#### Resources\n* VEP\n\n#### Conditions\n* \"transcript_consequence_terms\" is \"inframe_insertion\", \"inframe_deletion\", or \"stop_lost\".\n\n#### Shortcomings\n* No checks for repeat regions.\n\n### PM5\n* Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before\n\n#### Status\n* Broken. (\u256f\u00b0\u25a1\u00b0\uff09\u256f\ufe35 \u253b\u2501\u253b)\n\n#### Resources\n* Clinvar xml (ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/)\n\n#### Annotation Steps\n1. Clinvar data is parsed using https://github.com/barslmn/clinvar.\n2. Sample data and clinvar data hgvsp columns parsed till position.\n3. Synonym changes removed from clinvar data.\n4. Clinvar feature columns \"hgvsc\", and \"clinical_significance\" added to original annotation based on protein change position.\n\n#### Conditions\n1. \"gnomad\" less then 0.001.\n2. \"clinical_significance\" is pathogenic.\n3. \"transcript_consequence_terms\" is missense variant.\n4. \"hgvsc\" of the variant and clinvar entry dont match.\n\n#### Shortcomings\n\n### PM6\n* Assumed de novo, but without confirmation of paternity and maternity\n\n#### Status\n* Planned for trio.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PP1\n* Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease\n\n#### Status\n* Planned after Vesta.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PP2\n* 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\n\n#### Status\n* Implemented\n\n#### Resources\n* Intervar\n\n#### Conditions\n* \"transcript_consequence_terms\" is a missense variant.\n* \"gene_symbol\" is in PP2 gene list.\n\n#### Shortcomings\n\n### PP3\n* Multiple\u2002lines\u2002of\u2002computational\u2002evidence\u2002support\u2002a\u2002deleterious\u2002effect\u2002on\u2002the\u2002gene\u2002or\u2002gene\u2002product\u2002(conservation, evolutionary, splicing impact, etc.)\n\n#### Status\n* Implemented\n\n#### Resources\n* Vep\n\n#### Conditions\n* \"sift_score\" less than 0.05\n* \"polyphen_score\" greater than 0.908\n\n#### Shortcomings\n\n### PP4\n* Patient\u2019s phenotype or family history is highly specific for a disease with a single genetic etiology\n\n#### Status\n* Not Checked.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### PP5\n* Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation\n\n#### Status\n* Implemented.\n\n#### Resources\n* Clinvar\n\n#### Conditions\n* \"clinical_significance\" is Pathogenic.\n\n#### Shortcomings\n\n### Benign\n\n### BA1\n* Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium\n\n#### Status\n* Implemented.\n\n#### Resources\n* Vep\n\n#### Conditions\n* \"minor_allele_freq\" is greater than 0.05\n\nOR\n\n* \"gnomad\" is greater than 0.05.\n\n#### Shortcomings\n\n### BS1\n* Allele frequency is greater than expected for disorder\n\n#### Status\n* Planned for later.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### BS2\n* Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age\n\n#### Status\n* Planned\n\n#### Resources\n* Intervar\n\n#### Conditions\n\n#### Shortcomings\n\n### BS3\n* Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing\n\n#### Status\n* Not Checked.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### BS4\n* Lack of segregation in affected members of a family\n\n#### Status\n* Not Checked.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### BP1\n* Missense variant in a gene for which primarily truncating variants are known to cause disease\n\n#### Status\n* Implemented.\n\n#### Resources\n* Intervar\n\n#### Conditions\n* \"transcript_consequence_terms\" is a missense variant.\n* \"gene_symbol\" is in BP1 gene list.\n\n#### Shortcomings\n\n### BP2\n* Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern\n\n#### Status\n* Planned for trio.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### BP3\n* In-frame\u2002deletions/insertions\u2002in\u2002a\u2002repetitive\u2002region\u2002without\u2002a\u2002known\u2002function\n\n#### Status\n* Not Checked.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### BP4\n* Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)\n\n#### Status\n* Implemented\n\n#### Resources\n* VEP\n\n#### Conditions\n* \"sift_score\" greater than or equals to 0.05\n* \"polyphen_score\" less than or equals to 0.446\n\n#### Shortcomings\n\n### BP5\n* Variant found in a case with an alternate molecular basis for disease\n\n#### Status\n* Not Checked.\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n### BP6\n* Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation\n\n#### Status\n* Implemented\n\n#### Resources\n* Clinvar\n\n#### Conditions\n* \"clinical_significance\" is benign\n\n#### Shortcomings\n\n### BP7\n* A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved\n\n#### Status\n* Planned\n\n#### Resources\n\n#### Conditions\n\n#### Shortcomings\n\n\n",
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