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UnknownAssessment of the evidence yield for the calibrated PP3/BP4 computational recommendations.

Purpose

To investigate the number of rare missense variants observed in human genome sequences by ACMG/AMP PP3/BP4 evidence strength, following the ClinGen-calibrated PP3/BP4 computational recommendations.

Methods

Missense variants from the genome sequences of 300 probands from the Ra...
S-EPMC11560577 | biostudies-literature
UnknownCalibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.
Recommendations from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) for interpreting sequence variants specify the use of computational predictors as "supporting" level of evidence for pathogenicity or benignity using criteria PP3 and BP4...
S-EPMC9748256 | biostudies-literature
UnknownClassification of BRCA1 missense variants of unknown clinical significance.

Background

BRCA1 is a tumour suppressor with pleiotropic actions. Germline mutations in BRCA1 are responsible for a large proportion of breast-ovarian cancer families. Several missense variants have been identified throughout the gene but because of lack of information about their impact on ...
S-EPMC1735988 | biostudies-literature
UnknownA unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.
High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (...
S-EPMC4157619 | biostudies-literature
UnknownLarge-scale application of ClinGen-InSiGHT APC-specific ACMG/AMP variant classification criteria leads to substantial reduction in VUS.
Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUSs), APC-specific variant classificatio...
S-EPMC11568752 | biostudies-literature
UnknownGene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel.

Purpose

The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variant...
S-EPMC10922469 | biostudies-literature
UnknownApplication of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and appl...
S-EPMC4294709 | biostudies-literature
UnknownNo evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

Background

BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating va...
S-EPMC4938802 | biostudies-literature
UnknownLarge scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification.
The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probab...
S-EPMC6772163 | biostudies-literature
UnknownPALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS.

Background

The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rar...
S-EPMC5200636 | biostudies-literature
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