id stringlengths 21 21 | kind stringclasses 3
values | options listlengths 2 6 | target listlengths 2 6 | state stringlengths 161 260 | question stringclasses 7
values | domain stringclasses 1
value | family stringclasses 1
value | source stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|
v3_3ab08146dbefc7da_n | noul | [
"false",
"true"
] | [
0.21,
0.79
] | An ldlr variant creates a premature stop codon; additionally segregates with disease in the family. Context: de novo in the proband, with staffing at reduced levels. Reported by the operator. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_2a31a35cf870cff6_n | noul | [
"false",
"true"
] | [
0.71,
0.29
] | An ldlr variant is a missense change in a conserved domain; additionally has a CADD score of 34. Context: in an unaffected 70-year-old relative, with staffing at reduced levels. Reported by the supervisor. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_86012332c9f4c6d2_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.05,
0.57,
0.36,
0.01
] | A cftr mutation has a CADD score of 34; additionally has conflicting functional studies. Context: de novo in the proband, during normal operations. Reported by the monitoring system. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_02ed4547cbfa206f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.09,
0.27,
0.6,
0.03,
0
] | A brca1 variant is absent from population databases at 0.0004 frequency; additionally is a missense change in a conserved domain. Context: in an unaffected 70-year-old relative, during peak load. Reported by the operator. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_ce25ce7f999a8b40_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.21,
0.64,
0.14,
0
] | A cftr mutation appears in ClinVar as pathogenic with 2-star review; additionally creates a premature stop codon. Context: in a screening-only context, during the morning shift. Reported by the operator. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_4a7db0698cb9e9eb_n | noul | [
"false",
"true"
] | [
0.8,
0.2
] | An ldlr variant has conflicting functional studies; additionally matches the reference sequence exactly. Context: in a patient with the phenotype, with a new vendor onboarded. Reported by the monitoring system. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_a9c481f466fc826c_n | noul | [
"false",
"true"
] | [
0.39,
0.61
] | An ldlr variant has conflicting functional studies; additionally segregates with disease in the family. Context: in an unaffected 70-year-old relative, during peak load. Reported by the on-call engineer. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_c8a41f8398a79ff2_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.01,
0.54,
0.07,
0.38
] | A cftr mutation matches the reference sequence exactly; additionally causes a frameshift at codon 1200. Context: in an unaffected 70-year-old relative, with staffing at reduced levels. Reported by the on-call engineer. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_ce36c3c9621c747d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.04,
0.76,
0.2,
0
] | An ldlr variant has conflicting functional studies; additionally has a CADD score of 34. Context: de novo in the proband, during the quarterly review. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_e2179abc58a4ed0a_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.09,
0.52,
0.01,
0.38
] | A tp53 variant matches the reference sequence exactly; additionally creates a premature stop codon. Context: de novo in the proband, following a recent audit. Reported by the supervisor. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_aa15e4c66cef29ec_n | noul | [
"false",
"true"
] | [
0.3,
0.7
] | A cftr mutation is absent from population databases at 0.0004 frequency; additionally is a missense change in a conserved domain. Context: de novo in the proband, with staffing at reduced levels. Reported by the monitoring system. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_eb8e7b852efe2d28_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.03,
0.05,
0.15,
0.37,
0.38,
0.02
] | A tp53 variant causes a frameshift at codon 1200; additionally matches the reference sequence exactly. Context: in a patient with the phenotype, while on-call rotation changed. Reported by the review queue. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_34e0cda1469550e3_n | noul | [
"false",
"true"
] | [
0.76,
0.24
] | An ldlr variant is absent from population databases at 0.0004 frequency; additionally has conflicting functional studies. Context: in an unaffected 70-year-old relative, during the morning shift. Reported by the review queue. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_4f986136cae20c3e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.04,
0.14,
0.54,
0.27,
0.01
] | A brca1 variant appears in ClinVar as pathogenic with 2-star review; additionally creates a premature stop codon. Context: in an unaffected 70-year-old relative, at the end of the fiscal period. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_e66949268c682da2_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.29,
0.36,
0.28,
0.05,
0
] | An ldlr variant has a CADD score of 34; additionally is a silent change with no splice impact. Context: de novo in the proband, mid-incident. Reported by the operator. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_d354720f02c8da49_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.01,
0.01,
0.09,
0.63,
0.25
] | An ldlr variant is a missense change in a conserved domain; additionally causes a frameshift at codon 1200. Context: in a screening-only context, under an active deadline. Reported by the on-call engineer. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_000979895bbfaa41_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0,
0.01,
0.48,
0.51
] | A brca1 variant has conflicting functional studies; additionally is a silent change with no splice impact. Context: in an unaffected 70-year-old relative, mid-incident. Reported by the on-call engineer. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_c0f1e58c7f02e137_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.02,
0.14,
0.68,
0.15
] | A brca1 variant causes a frameshift at codon 1200; additionally creates a premature stop codon. Context: in a screening-only context, during an external partner integration. Reported by the review queue. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_64d1d81f8377c588_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.11,
0.07,
0.5,
0.32
] | An ldlr variant matches the reference sequence exactly; additionally causes a frameshift at codon 1200. Context: in a screening-only context, shortly after a software update. Reported by the supervisor. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_761f68d2e9ef6c06_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.58,
0.3,
0.11,
0.01
] | A cftr mutation segregates with disease in the family; additionally creates a premature stop codon. Context: in a screening-only context, shortly after a software update. Reported by the monitoring system. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_8724948b482a3637_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.04,
0.44,
0.5,
0.02
] | A brca1 variant appears in ClinVar as pathogenic with 2-star review; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, immediately after go-live. Reported by the review queue. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_aca082edb71776bf_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.21,
0.28,
0.5,
0.01
] | An ldlr variant is absent from population databases at 0.0004 frequency; additionally has conflicting functional studies. Context: de novo in the proband, mid-incident. Reported by the operator. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_5e7a22be5a522b11_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.1,
0.36,
0.54,
0
] | A brca1 variant has a CADD score of 34; additionally has conflicting functional studies. Context: de novo in the proband, during peak load. Reported by the automated check. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_c770ab769b0bc307_n | noul | [
"false",
"true"
] | [
0.75,
0.25
] | A brca1 variant segregates with disease in the family; additionally is a silent change with no splice impact. Context: in a patient with the phenotype, with a new vendor onboarded. Reported by the monitoring system. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_f38f5df51d45ad2f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.11,
0.18,
0.18,
0.29,
0.21,
0.03
] | An ldlr variant matches the reference sequence exactly; additionally has a CADD score of 34. Context: de novo in the proband, with staffing at reduced levels. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_4f32745f16ac09f1_n | noul | [
"false",
"true"
] | [
0.51,
0.49
] | A brca1 variant segregates with disease in the family; additionally is a silent change with no splice impact. Context: in a patient with the phenotype, during normal operations. Reported by the on-call engineer. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_f034d1dd08320936_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.12,
0.79,
0.08
] | A brca1 variant causes a frameshift at codon 1200; additionally has a CADD score of 34. Context: in a patient with the phenotype, while on-call rotation changed. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_5425ee00b6756b15_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.2,
0.25,
0.5,
0.05
] | A tp53 variant is a missense change in a conserved domain; additionally causes a frameshift at codon 1200. Context: in a screening-only context, shortly after a software update. Reported by the review queue. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_8f97805b7efb2ad3_n | noul | [
"false",
"true"
] | [
0.74,
0.26
] | A tp53 variant has a CADD score of 34; additionally matches the reference sequence exactly. Context: in a screening-only context, at the end of the fiscal period. Reported by the monitoring system. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_090b9e8b643c6bfd_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.1,
0.23,
0.07,
0.6
] | A tp53 variant has a CADD score of 34; additionally has conflicting functional studies. Context: in an unaffected 70-year-old relative, during the quarterly review. Reported by the review queue. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_2d7de8e421a5431c_n | noul | [
"false",
"true"
] | [
0.24,
0.76
] | A tp53 variant segregates with disease in the family; additionally appears in ClinVar as pathogenic with 2-star review. Context: de novo in the proband, during the quarterly review. Reported by the review queue. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_a043b7203c19d675_n | noul | [
"false",
"true"
] | [
0.75,
0.25
] | A cftr mutation is absent from population databases at 0.0004 frequency; additionally has conflicting functional studies. Context: in a screening-only context, with a new vendor onboarded. Reported by the automated check. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_9ea47f5b6b01425c_n | noul | [
"false",
"true"
] | [
0.41,
0.59
] | A tp53 variant is absent from population databases at 0.0004 frequency; additionally segregates with disease in the family. Context: in a screening-only context, during the morning shift. Reported by the automated check. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_380d3c001b9dac70_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.06,
0.13,
0.06,
0.75
] | A tp53 variant has a CADD score of 34; additionally has conflicting functional studies. Context: in an unaffected 70-year-old relative, under an active deadline. Reported by the automated check. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_eb433cc7ad4c032e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.48,
0.51,
0
] | An ldlr variant is a missense change in a conserved domain; additionally is absent from population databases at 0.0004 frequency. Context: in a patient with the phenotype, during the system migration. Reported by the monitoring system. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_adc970bc7abc54bd_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.17,
0.77,
0.05
] | A brca1 variant has a CADD score of 34; additionally is absent from population databases at 0.0004 frequency. Context: de novo in the proband, at the end of the fiscal period. Reported by the automated check. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_bc09c98df881e418_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.05,
0.11,
0.42,
0.39,
0.02
] | A brca1 variant causes a frameshift at codon 1200; additionally is absent from population databases at 0.0004 frequency. Context: in an unaffected 70-year-old relative, during normal operations. Reported by the review queue. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_8015ab0e8d1a2abb_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.01,
0.25,
0.66,
0.08
] | A tp53 variant is absent from population databases at 0.0004 frequency; additionally is a missense change in a conserved domain. Context: in an unaffected 70-year-old relative, during the morning shift. Reported by the operator. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_0974e5130605ff91_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.88,
0.1,
0,
0.02
] | An ldlr variant has conflicting functional studies; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, mid-incident. Reported by the monitoring system. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_a94e52f41bf29a84_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.01,
0.97,
0.02,
0
] | A tp53 variant segregates with disease in the family; additionally has conflicting functional studies. Context: in an unaffected 70-year-old relative, during the system migration. Reported by the monitoring system. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_b38ee09a932b3ac5_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.05,
0.63,
0.32,
0
] | A tp53 variant causes a frameshift at codon 1200; additionally has conflicting functional studies. Context: in a screening-only context, during the quarterly review. Reported by the on-call engineer. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_6100bc3dc618ecde_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.11,
0.02,
0.02,
0.04,
0.38,
0.43
] | A cftr mutation creates a premature stop codon; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, during a scheduled maintenance window. Reported by the on-call engineer. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_3e80fb7238726f03_n | noul | [
"false",
"true"
] | [
0.66,
0.34
] | A cftr mutation is a silent change with no splice impact; additionally appears in ClinVar as pathogenic with 2-star review. Context: in an unaffected 70-year-old relative, as part of a compliance sweep. Reported by the operator. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_d266330b98b5418d_n | noul | [
"false",
"true"
] | [
0.27,
0.73
] | A tp53 variant causes a frameshift at codon 1200; additionally segregates with disease in the family. Context: in a patient with the phenotype, at the end of the fiscal period. Reported by the on-call engineer. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_6510117cf73949c2_n | noul | [
"false",
"true"
] | [
0.44,
0.56
] | A brca1 variant appears in ClinVar as pathogenic with 2-star review; additionally segregates with disease in the family. Context: in an unaffected 70-year-old relative, during normal operations. Reported by the automated check. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_2072bd5d2bcc2ba1_n | noul | [
"false",
"true"
] | [
0.75,
0.25
] | An ldlr variant has conflicting functional studies; additionally is a missense change in a conserved domain. Context: in an unaffected 70-year-old relative, shortly after a software update. Reported by the supervisor. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_b69a989229a8c6e3_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.06,
0.13,
0.18,
0.55,
0.08,
0
] | A tp53 variant has conflicting functional studies; additionally is absent from population databases at 0.0004 frequency. Context: in an unaffected 70-year-old relative, shortly after a software update. Reported by the monitoring system. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_c5d8b6ce0fcaf669_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.03,
0.41,
0.55,
0.01
] | A brca1 variant causes a frameshift at codon 1200; additionally appears in ClinVar as pathogenic with 2-star review. Context: in a patient with the phenotype, during normal operations. Reported by the supervisor. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_d041081abb14f36d_n | noul | [
"false",
"true"
] | [
0.19,
0.81
] | A brca1 variant has a CADD score of 34; additionally segregates with disease in the family. Context: in a patient with the phenotype, while legacy systems are still active. Reported by the supervisor. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_7d447f99eed7b33b_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.01,
0.23,
0.48,
0.28
] | A brca1 variant is a missense change in a conserved domain; additionally is absent from population databases at 0.0004 frequency. Context: de novo in the proband, mid-incident. Reported by the operator. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_eebc78b8918ca3e9_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.35,
0.41,
0.24,
0
] | A cftr mutation causes a frameshift at codon 1200; additionally is a missense change in a conserved domain. Context: de novo in the proband, during peak load. Reported by the supervisor. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_128aedcd85c83983_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.01,
0,
0.71,
0.28
] | A tp53 variant is a silent change with no splice impact; additionally is absent from population databases at 0.0004 frequency. Context: in a screening-only context, with a new vendor onboarded. Reported by the on-call engineer. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_b48288d5e0916e13_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.05,
0.24,
0.71,
0
] | An ldlr variant causes a frameshift at codon 1200; additionally has conflicting functional studies. Context: in a screening-only context, while on-call rotation changed. Reported by the on-call engineer. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_45f6a1873684fde6_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.0707,
0.8182,
0.1111,
0
] | A tp53 variant has conflicting functional studies; additionally segregates with disease in the family. Context: in a patient with the phenotype, during normal operations. Reported by the monitoring system. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_9167daa635f14cc0_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.02,
0.02,
0.11,
0.74,
0.09
] | A brca1 variant has a CADD score of 34; additionally creates a premature stop codon. Context: in a patient with the phenotype, shortly after a software update. Reported by the review queue. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_0267bab181d61d71_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.11,
0.53,
0.01,
0.35
] | A tp53 variant is a missense change in a conserved domain; additionally creates a premature stop codon. Context: de novo in the proband, under an active deadline. Reported by the monitoring system. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_884c7b39e416fab1_n | noul | [
"false",
"true"
] | [
0.71,
0.29
] | An ldlr variant segregates with disease in the family; additionally matches the reference sequence exactly. Context: in a patient with the phenotype, during peak load. Reported by the review queue. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_e992cfb68e585b06_n | noul | [
"false",
"true"
] | [
0.45,
0.55
] | An ldlr variant segregates with disease in the family; additionally has conflicting functional studies. Context: de novo in the proband, during peak load. Reported by the operator. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_b21098d56718473c_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.14,
0.17,
0.28,
0.41
] | A cftr mutation creates a premature stop codon; additionally appears in ClinVar as pathogenic with 2-star review. Context: in an unaffected 70-year-old relative, during the quarterly review. Reported by the supervisor. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_1f77f48ef07199d8_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.0202,
0.101,
0.1717,
0.2727,
0.3939,
0.0404
] | An ldlr variant causes a frameshift at codon 1200; additionally creates a premature stop codon. Context: in an unaffected 70-year-old relative, following a recent audit. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_39d562a52a37a1cb_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.06,
0.09,
0.37,
0.48
] | An ldlr variant is absent from population databases at 0.0004 frequency; additionally matches the reference sequence exactly. Context: in a patient with the phenotype, mid-incident. Reported by the review queue. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_cdda4719d6bc0608_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.21,
0.61,
0.18,
0
] | A cftr mutation has conflicting functional studies; additionally creates a premature stop codon. Context: in a screening-only context, under an active deadline. Reported by the supervisor. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_58c120080aacb249_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.24,
0.06,
0.31,
0.39
] | A brca1 variant is a missense change in a conserved domain; additionally causes a frameshift at codon 1200. Context: de novo in the proband, shortly after a software update. Reported by the on-call engineer. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_2053caa6c1cad839_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.09,
0.61,
0.28,
0.01
] | A tp53 variant has a CADD score of 34; additionally has conflicting functional studies. Context: in a screening-only context, during peak load. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_af447a4c534925f3_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.2,
0.71,
0.08
] | An ldlr variant creates a premature stop codon; additionally segregates with disease in the family. Context: in a patient with the phenotype, following a recent audit. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_e564d4bc3311d812_n | noul | [
"false",
"true"
] | [
0.8,
0.2
] | A tp53 variant has a CADD score of 34; additionally matches the reference sequence exactly. Context: de novo in the proband, following a recent audit. Reported by the on-call engineer. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_2f8fe28ba7df1a6e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.01,
0.11,
0.78,
0.09,
0
] | A cftr mutation appears in ClinVar as pathogenic with 2-star review; additionally has conflicting functional studies. Context: de novo in the proband, during the morning shift. Reported by the review queue. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_ab679f7aafac6ddb_n | noul | [
"false",
"true"
] | [
0.16,
0.84
] | A cftr mutation creates a premature stop codon; additionally appears in ClinVar as pathogenic with 2-star review. Context: in a patient with the phenotype, following a recent audit. Reported by the monitoring system. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_66b48caaa3b62c05_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.02,
0.2,
0.71,
0.07
] | A brca1 variant is absent from population databases at 0.0004 frequency; additionally creates a premature stop codon. Context: de novo in the proband, during the morning shift. Reported by the on-call engineer. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_5b6d6b812ca01cb4_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.71,
0.27,
0.02,
0
] | A brca1 variant creates a premature stop codon; additionally segregates with disease in the family. Context: in a patient with the phenotype, while on-call rotation changed. Reported by the monitoring system. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_59e5a15aa30ecea2_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0,
0.01,
0.75,
0.24
] | A brca1 variant is a silent change with no splice impact; additionally has conflicting functional studies. Context: de novo in the proband, while on-call rotation changed. Reported by the monitoring system. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_b622ed1ee9e5a3dc_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0,
0.01,
0.1,
0.77,
0.11
] | A tp53 variant causes a frameshift at codon 1200; additionally is a missense change in a conserved domain. Context: in a patient with the phenotype, following a recent audit. Reported by the on-call engineer. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_51d01288db79b22f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.1717,
0.1414,
0.1717,
0.202,
0.2828,
0.0303
] | A brca1 variant is a silent change with no splice impact; additionally causes a frameshift at codon 1200. Context: de novo in the proband, shortly after a software update. Reported by the review queue. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_5201301e7c7c5b7d_n | noul | [
"false",
"true"
] | [
0.3,
0.7
] | A tp53 variant creates a premature stop codon; additionally is absent from population databases at 0.0004 frequency. Context: in a patient with the phenotype, shortly after a software update. Reported by the monitoring system. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_38c9348c38ea911e_n | noul | [
"false",
"true"
] | [
0.45,
0.55
] | A tp53 variant is absent from population databases at 0.0004 frequency; additionally appears in ClinVar as pathogenic with 2-star review. Context: in an unaffected 70-year-old relative, while legacy systems are still active. Reported by the review queue. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_4258bcbefeb38c90_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.01,
0.04,
0.24,
0.64,
0.06
] | A cftr mutation has a CADD score of 34; additionally creates a premature stop codon. Context: in a screening-only context, with a new vendor onboarded. Reported by the on-call engineer. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_24ec76450f8676e9_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.03,
0.66,
0.31,
0
] | A tp53 variant segregates with disease in the family; additionally has conflicting functional studies. Context: de novo in the proband, during the quarterly review. Reported by the monitoring system. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_041f86c2874571cd_n | noul | [
"false",
"true"
] | [
0.18,
0.82
] | An ldlr variant causes a frameshift at codon 1200; additionally has a CADD score of 34. Context: in a patient with the phenotype, under an active deadline. Reported by the on-call engineer. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_946bab026bbabe2b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.04,
0.07,
0.3,
0.53,
0.05
] | A cftr mutation has a CADD score of 34; additionally segregates with disease in the family. Context: in an unaffected 70-year-old relative, under an active deadline. Reported by the supervisor. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_6f7185d06bff7dd1_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0,
0,
0.93,
0.07
] | A cftr mutation is absent from population databases at 0.0004 frequency; additionally matches the reference sequence exactly. Context: in a screening-only context, following a recent audit. Reported by the operator. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_eeb2d910f01b7161_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.02,
0.38,
0.58,
0.02
] | A tp53 variant appears in ClinVar as pathogenic with 2-star review; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, at the end of the fiscal period. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_54b156e39d961ff9_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.02,
0.15,
0.59,
0.23,
0
] | A tp53 variant is a missense change in a conserved domain; additionally matches the reference sequence exactly. Context: de novo in the proband, mid-incident. Reported by the supervisor. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_0d24fbbcdaf65c06_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0,
0.9,
0,
0.1
] | A tp53 variant segregates with disease in the family; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, shortly after a software update. Reported by the automated check. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_9f2d236f0970d39a_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.04,
0.14,
0.65,
0.16,
0
] | An ldlr variant is a silent change with no splice impact; additionally is a missense change in a conserved domain. Context: de novo in the proband, during peak load. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_264960520dd624bd_n | noul | [
"false",
"true"
] | [
0.79,
0.21
] | A tp53 variant has conflicting functional studies; additionally matches the reference sequence exactly. Context: de novo in the proband, during the system migration. Reported by the supervisor. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_a7dbb6318b7ccbab_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.06,
0.71,
0.22,
0
] | A tp53 variant is a missense change in a conserved domain; additionally is absent from population databases at 0.0004 frequency. Context: in a screening-only context, during peak load. Reported by the automated check. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_b0d14100038545cf_n | noul | [
"false",
"true"
] | [
0.65,
0.35
] | A tp53 variant creates a premature stop codon; additionally matches the reference sequence exactly. Context: in an unaffected 70-year-old relative, during peak load. Reported by the automated check. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_264731dd966fabc6_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.49,
0.44,
0.07,
0
] | A tp53 variant causes a frameshift at codon 1200; additionally appears in ClinVar as pathogenic with 2-star review. Context: in a patient with the phenotype, under an active deadline. Reported by the monitoring system. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_86bafdc04f0c47fe_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.06,
0.38,
0.44,
0.09,
0.01
] | A tp53 variant is a silent change with no splice impact; additionally is a missense change in a conserved domain. Context: in a patient with the phenotype, during the morning shift. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_3337cf215ae1cf6b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.05,
0.2,
0.72,
0.03,
0
] | A brca1 variant has conflicting functional studies; additionally is absent from population databases at 0.0004 frequency. Context: in an unaffected 70-year-old relative, during the system migration. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_bd333d77158c328e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.03,
0.29,
0.34,
0.3,
0.04,
0
] | A cftr mutation is a silent change with no splice impact; additionally segregates with disease in the family. Context: de novo in the proband, during peak load. Reported by the automated check. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_5d3a0e6b1bd3732f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.02,
0.12,
0.57,
0.29,
0
] | A tp53 variant is a silent change with no splice impact; additionally is a missense change in a conserved domain. Context: de novo in the proband, during normal operations. Reported by the monitoring system. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_dc260f54987a2f6d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.16,
0.43,
0.25,
0.1,
0.05,
0.01
] | A brca1 variant matches the reference sequence exactly; additionally segregates with disease in the family. Context: in a patient with the phenotype, during a scheduled maintenance window. Reported by the review queue. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_1404f4c78f9ad97c_n | noul | [
"false",
"true"
] | [
0.45,
0.55
] | A brca1 variant causes a frameshift at codon 1200; additionally matches the reference sequence exactly. Context: in an unaffected 70-year-old relative, during the quarterly review. Reported by the review queue. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_0dbc44bec78e02d8_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.04,
0.18,
0.68,
0.1,
0
] | A tp53 variant is absent from population databases at 0.0004 frequency; additionally appears in ClinVar as pathogenic with 2-star review. Context: in an unaffected 70-year-old relative, with staffing at reduced levels. Reported by the on-call engineer. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_346a1391a3126a3a_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.87,
0.12,
0
] | An ldlr variant has conflicting functional studies; additionally is a missense change in a conserved domain. Context: de novo in the proband, during the quarterly review. Reported by the monitoring system. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_e8ae8fe7ca0a1236_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.11,
0.2,
0.5,
0.18,
0.01,
0
] | A tp53 variant is a silent change with no splice impact; additionally is a missense change in a conserved domain. Context: in an unaffected 70-year-old relative, during the system migration. Reported by the on-call engineer. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_d140add4fae10b96_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.1111,
0.8182,
0.0303,
0.0202,
0.0101,
0.0101
] | A cftr mutation matches the reference sequence exactly; additionally is a silent change with no splice impact. Context: in an unaffected 70-year-old relative, at the end of the fiscal period. Reported by the supervisor. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_c7ef588dc4d6445b_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.71,
0.18,
0.09,
0.02
] | A cftr mutation creates a premature stop codon; additionally is a silent change with no splice impact. Context: in a screening-only context, with staffing at reduced levels. Reported by the review queue. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_d0f9c6183baf1c7b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.02,
0.1,
0.3,
0.54,
0.03
] | A cftr mutation is a silent change with no splice impact; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, during the morning shift. Reported by the automated check. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
End of preview. Expand in Data Studio
JEV corpus - variant_interpretation
7,903 typed calibrated decision rows from the jev-distill-corpus-v3 corpus (domain: variant_interpretation).
Each row is one typed decision: kind (noul / choice / score), a state, a question, options, and a target probability distribution over the options.
Part of the per-domain split of SargeDev/jev-distill-corpus-v3 - the full corpus in one repo.
Domains:
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