[Paper-level Aggregated] PMCID: PMC7611203

Evidence Type(s): Oncogenic

Summary: Mutation: c.7355delA | Summary: The mutation c.7355delA in BRCA2 is described as a pathogenic mutation, indicating its contribution to tumor development or progression.

Evidence Type: Oncogenic Mutation: p.C61S | Summary: The BRCA1:p.C61S missense mutation is described as pathogenic, indicating it contributes to tumor development or progression.

Evidence Type: Oncogenic Mutation: p.M1I | Summary: The BRCA1:p.M1I pathogenic mutation is noted to result in loss of the translation start site, suggesting it contributes to tumor development or progression.

Evidence Type: Oncogenic Mutation: c.5946delT | Summary: The BRCA2:c.5946delT mutation is described as pathogenic and is associated with the presentation of neoantigens, indicating its contribution to tumor development.

Evidence Type: Oncogenic Mutation: c.68_69delAG | Summary: The BRCA1:c.68_69delAG mutation is identified as pathogenic and is linked to the generation of neoantigens, suggesting its role in tumor progression.

Evidence Type: Oncogenic Mutation: c.5266dupC | Summary: The BRCA1:c.5266dupC mutation is classified as pathogenic and is associated with neoantigen presentation, indicating its involvement in tumor development.

Gene→Variant (gene-first): BRCA2(675):c.7355delA BRCA1(672):p.C61S BRCA1(672):p.M1I BRCA2(675):c.5946delT BRCA1(672):c.68_69delAG BRCA1(672):c.5266dupC

Genes: BRCA2(675) BRCA1(672)

Variants: c.7355delA p.C61S p.M1I c.5946delT c.68_69delAG c.5266dupC

[Paper-level Aggregated] PMCID: PMC7611203

Evidence Type(s): Diagnostic

Summary: Mutation: c.185delAG | Summary: The BRCA1:c.185delAG mutation is mentioned as a pathogenic mutation used to classify patients in the dataset, indicating its role in defining a disease subtype.

Evidence Type: Diagnostic Mutation: c.5946delT | Summary: The BRCA2:c.5946delT mutation is identified as a common founder mutation in multiple patients, supporting its use in disease classification.

Evidence Type: Diagnostic Mutation: c.6174delT | Summary: The BRCA2:c.6174delT mutation is noted as a pathogenic mutation represented by multiple patients, indicating its role in defining a disease subtype.

Gene→Variant (gene-first): BRCA1(672):c.185delAG BRCA2(675):c.5946delT BRCA2(675):c.6174delT

Genes: BRCA1(672) BRCA2(675)

Variants: c.185delAG c.5946delT c.6174delT

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 26

Evidence Type(s): Oncogenic

Summary: Evidence Type: Oncogenic | Mutation: c.5946delT | Summary: The BRCA2:c.5946delT mutation is described as pathogenic and is associated with the presentation of neoantigens, indicating its contribution to tumor development. Evidence Type: Oncogenic | Mutation: c.68_69delAG | Summary: The BRCA1:c.68_69delAG mutation is identified as pathogenic and is linked to the generation of neoantigens, suggesting its role in tumor progression. Evidence Type: Oncogenic | Mutation: c.5266dupC | Summary: The BRCA1:c.5266dupC mutation is classified as pathogenic and is associated with neoantigen presentation, indicating its involvement in tumor development.

Gene→Variant (gene-first): 672:c.5266dupC 675:c.5946delT 672:c.68_69delAG

Genes: 672 675

Variants: c.5266dupC c.5946delT c.68_69delAG

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 16

Evidence Type(s): Oncogenic

Summary: Evidence Type: Oncogenic | Mutation: p.C61S | Summary: The BRCA1:p.C61S missense mutation is described as pathogenic, indicating it contributes to tumor development or progression. Evidence Type: Oncogenic | Mutation: p.M1I | Summary: The BRCA1:p.M1I pathogenic mutation is noted to result in loss of the translation start site, suggesting it contributes to tumor development or progression.

Gene→Variant (gene-first): 672:p.C61S 672:p.M1I

Genes: 672

Variants: p.C61S p.M1I

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 8

Evidence Type(s): Oncogenic

Summary: Evidence Type: Oncogenic | Mutation: c.7355delA | Summary: The mutation c.7355delA in BRCA2 is described as a pathogenic mutation, indicating its contribution to tumor development or progression.

Gene→Variant (gene-first): 675:c.7355delA

Genes: 675

Variants: c.7355delA

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: c.185delAG | Summary: The BRCA1:c.185delAG mutation is mentioned as a pathogenic mutation used to classify patients in the dataset, indicating its role in defining a disease subtype. Evidence Type: Diagnostic | Mutation: c.5946delT | Summary: The BRCA2:c.5946delT mutation is identified as a common founder mutation in multiple patients, supporting its use in disease classification. Evidence Type: Diagnostic | Mutation: c.6174delT | Summary: The BRCA2:c.6174delT mutation is noted as a pathogenic mutation represented by multiple patients, indicating its role in defining a disease subtype.

Gene→Variant (gene-first): 672:c.185delAG 672:c.5266dupC 675:c.5946delT 675:c.6174delT 672:c.68_69delAG

Genes: 672 675

Variants: c.185delAG c.5266dupC c.5946delT c.6174delT c.68_69delAG

[Paper-level Aggregated] PMCID: PMC7611203

Evidence Type(s): Oncogenic, Predictive, Predisposing

Justification: Oncogenic: The text discusses multiple pathogenic mutations, including BRCA1 and BRCA2 variants, which are known to be associated with an increased risk of breast and ovarian cancer, indicating their oncogenic potential. Predictive: The mention of neoantigens derived from pathogenic mutations being likely presented by HLA class I complexes suggests that these mutations can be used to predict immune responses, which is a predictive aspect in the context of cancer treatment. Predisposing: The identification of common founder mutations such as BRCA1:c.185delAG and BRCA2:c.6174delT indicates that these variants predispose individuals to developing certain cancers, thus classifying them as predisposing mutations.

Gene→Variant (gene-first): BRCA1(672):c.185delAG BRCA1(672):c.5266dupC BRCA2(675):c.5946delT BRCA2(675):c.6174delT BRCA1(672):c.68_69delAG BRCA1(672):p.C61S BRCA1(672):p.M1I

Genes: BRCA1(672) BRCA2(675)

Variants: c.185delAG c.5266dupC c.5946delT c.6174delT c.68_69delAG p.C61S p.M1I

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 26

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses common founder mutations such as BRCA2:c.5946delT and BRCA1:c.68_69delAG, indicating their association with neopeptides that are likely presented in the population, which relates to defining or classifying a disease. Oncogenic: The mention of pathogenic mutations and their associated neoantigens suggests that these variants contribute to tumor development or progression, as they are described as potential tumor antigens.

Gene→Variant (gene-first): 672:c.5266dupC 675:c.5946delT 672:c.68_69delAG

Genes: 672 675

Variants: c.5266dupC c.5946delT c.68_69delAG

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 16

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of pathogenic missense mutations, specifically mentioning the BRCA1:p.C61S and p.M1I mutations, in the context of their association with disease, indicating their role in defining or confirming a disease subtype. Oncogenic: The passage refers to the BRCA1:p.C61S and p.M1I mutations as pathogenic, suggesting that they contribute to tumor development or progression, which aligns with the definition of oncogenic variants.

Gene→Variant (gene-first): 672:p.C61S 672:p.M1I

Genes: 672

Variants: p.C61S p.M1I

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 8

Evidence Type(s): None

Justification: Not enough information in this passage.

Gene→Variant (gene-first): 675:c.7355delA

Genes: 675

Variants: c.7355delA

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of specific pathogenic mutations in patients, indicating their association with disease, which supports the use of these variants for classification and diagnosis. Oncogenic: The mention of pathogenic mutations suggests that these variants contribute to tumor development or progression, particularly in the context of BRCA1 and BRCA2 mutations associated with cancer.

Gene→Variant (gene-first): 672:c.185delAG 672:c.5266dupC 675:c.5946delT 675:c.6174delT 672:c.68_69delAG

Genes: 672 675

Variants: c.185delAG c.5266dupC c.5946delT c.6174delT c.68_69delAG

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of specific pathogenic mutations in patients, indicating their association with disease, which supports the use of these variants for classification and diagnosis. Oncogenic: The mention of pathogenic mutations suggests that these variants contribute to tumor development or progression, particularly in the context of BRCA1 and BRCA2 mutations associated with cancer.

Gene→Variant (gene-first): 672:c.185delAG 672:c.5266dupC 675:c.5946delT 675:c.6174delT 672:c.68_69delAG

Genes: 672 675

Variants: c.185delAG c.5266dupC c.5946delT c.6174delT c.68_69delAG