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Example output file #144

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Jul 18, 2024
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Example output file #144

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194 changes: 194 additions & 0 deletions src/bench/NM_000257.3(MYH7):c.3036C>T_output.csv
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Original file line number Diff line number Diff line change
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{
"pvs1":{
"name":"PVS1",
"prediction":"<AutoACMGPrediction.NotSet":1>,
"summary":"",
"description":"PVS1 prediction failed."
},
"ps1":{
"name":"PS1",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.",
"description":""
},
"ps2":{
"name":"PS2",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"ps3":{
"name":"PS3",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"ps4":{
"name":"PS4",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"pm1":{
"name":"PM1",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Counting pathogenic variants in the range of 50bp.The range is 23892794 - 23892844. =>
Found 0 Pathogenic variants. =>
Found less than 4 pathogenic variants.Checking if the variant is in a UniProt domain. =>
Check if the variant is in a UniProt domain.
Counting pathogenic variants in the UniProt domain. The range is 23892755 - 23892932. =>
Found less than 2 pathogenic variants in the UniProt domain. PM1 is not met.",
"description":""
},
"pm2":{
"name":"PM2",
"prediction":"<AutoACMGPrediction.Positive":5>,
"summary":"Check allele frequency for the control population.
Allele frequency: 0.001873719971626997.Allele frequency <= 1%: PM2 is met.Check zygosity.",
"description":""
},
"pm3":{
"name":"PM3",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"pm4":{
"name":"PM4",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Check consequences of the variant for PM4.
Variant consequence is not indel or stop-loss. PM4 and BP3 are not met.Check if the variant is in a repeat region.
Variant is in a repeat region.",
"description":""
},
"pm5":{
"name":"PM5",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.",
"description":""
},
"pm6":{
"name":"PM6",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"pp1":{
"name":"PP1",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"pp2":{
"name":"PP2",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Fetching transcript data. =>
Error occurred during PP2 and BP1 prediction. Error: Transcript data is not fully set. Cannot initialize the PVS1 class.",
"description":""
},
"pp3":{
"name":"PP3",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Checking Scores. =>
An error occurred during prediction. Error: Missing dbNSFP data.",
"description":""
},
"pp4":{
"name":"PP4",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"pp5":{
"name":"PP5",
"prediction":"<AutoACMGPrediction.Depricated":4>,
"summary":"",
"description":""
},
"ba1":{
"name":"BA1",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Check allele frequency for the control population.
Allele frequency: 0.001873719971626997.
Allele frequency <= 1%: PM2 is met.Check zygosity.",
"description":""
},
"bs1":{
"name":"BS1",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Check allele frequency for the control population.
Allele frequency: 0.001873719971626997.
Allele frequency <= 1%: PM2 is met.Check zygosity.",
"description":""
},
"bs2":{
"name":"BS2",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Check allele frequency for the control population.
Allele frequency: 0.001873719971626997.
Allele frequency <= 1%: PM2 is met.Check zygosity.",
"description":""
},
"bs3":{
"name":"BS3",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"bs4":{
"name":"BS4",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"bp1":{
"name":"BP1",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"",
"description":""
},
"bp2":{
"name":"BP2",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"bp3":{
"name":"BP3",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Check consequences of the variant for PM4.
Variant consequence is not indel or stop-loss. PM4 and BP3 are not met.Check if the variant is in a repeat region.
Variant is in a repeat region.",
"description":""
},
"bp4":{
"name":"BP4",
"prediction":"<AutoACMGPrediction.Negative":6>,
"summary":"Checking Scores. =>
An error occurred during prediction. Error: Missing dbNSFP data.",
"description":""
},
"bp5":{
"name":"BP5",
"prediction":"<AutoACMGPrediction.NotAutomated":3>,
"summary":"",
"description":""
},
"bp6":{
"name":"BP6",
"prediction":"<AutoACMGPrediction.Depricated":4>,
"summary":"",
"description":""
},
"bp7":{
"name":"BP7",
"prediction":"<AutoACMGPrediction.Positive":5>,
"summary":"Checking for pathogenic variants in the range of 2bp. =>
No pathogenic variants found in the range of 2bp. =>
Checking for proximity to splice site. =>
Variant is not within 2bp of a splice site. =>
Predicting splice site alterations using SpliceAI. =>
Variant is not a splice site alteration. BP7 is met.",
"description":""
}
}
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