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Please note this is a beta version of the ClinGen Evidence Repository. This resource is intended to provide access to variant level evidence used and applied by ClinGen Variant Curation Expert Panels in the classification of variants. In this beta version, the evidence is limited to curation notes and referenced literature (PMIDs).

For general information about ClinGen Expert Panels and Variant Curation please visit: Clinical Domain Working Groups. For specific inquiries regarding a variant classification or evidence curation (e.g. population database queried, segregation counts or other evidence used) or to submit general comments about the evidence repo, please email us.

The resource is undergoing updates and tesing. Should you encounter any issues regarding the data displayed, lack of functionality or other problems, please let us know so we can rectify these accordingly. Your help in this regard is greatly appreciated.

ClinGen CDH1 ACMG Specifications V2

Benign
Pathogenic
Stand Alone
Strong
Supporting
Supporting
Moderate
Strong
Very Strong
Population Data

Allele frequency is greater than expected for disorder
MAF cutoff of 0.2%
99.99% CI; subpopulation must have a minimum of five alleles present. BA1

Observed in a healthy adult individual for a dominant disorder with full penetrance expected at an early age
Variant seen in 3 or more individuals w/o DCG, SRC tumors, or LBC and whose families do not suggest HDGC BS2-Supporting

Prevalence of variant in affected individuals is significantly increased compared to controls.
One family meets HDGC criteria
This rule assumes 30% penetrance in individuals with pathogenic variants. For example, if the variant in observed in 3 families, at least one of those families need to meet criteria for HDGC in order to apply this rule. PS4 cannot be applied to variants that meet BS1 or BA1 PS4-Supporting

Absent in population databases
Less than one out of 100,000 alleles in gnomAD cohort ; if present in 2 or more individuals, must be present in less than one out of 50,000 alleles within a sub - population PM2

Prevalence of variant in affected individuals is significantly increased compared to controls.
Two families meet HDGC criteria
This rule assumes 30% penetrance in individuals with pathogenic variants. For example, if the variant in observed in 3 families, at least one of those families need to meet criteria for HDGC in order to apply this rule. PS4 cannot be applied to variants that meet BS1 or BA1 PS4-Moderate

Prevalence of variant in affected individuals is significantly increased compared to controls.
Four families meet HDGC criteria
This rule assumes 30% penetrance in individuals with pathogenic variants. For example, if the variant in observed in 3 families, at least one of those families need to meet criteria for HDGC in order to apply this rule. PS4 cannot be applied to variants that meet BS1 or BA1 PS4

Prevalence of variant in affected individuals is significantly increased compared to controls.
Sixteen families meet HDGC criteria
This rule assumes 30% penetrance in individuals with pathogenic variants. For example, if the variant in observed in 3 families, at least one of those families need to meet criteria for HDGC in order to apply this rule. PS4 cannot be applied to variants that meet BS1 or BA1 PS4-Very Strong

Computational And Predictive Data

Synonymous variant 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.
Synonymous variants where nucleotide is not highly conserved; variant is the reference nucleotide in one primate and/or 3 or more mammal species
Note the CDH1 rule specification does not require a benign in silico splice prediction. This allows use with BP4, as appropriate, to classify variants meeting both criteria as likely benign BP7

Multiple lines of computational evidence suggest no impact on gene/gene product
Splicing predictions only. At least three in silico splicing predictors in agreement (Human Splicing Finder (HSF), Maximum Entropy (MaxEnt), Berkeley Drosophilia Genome Project (BDGP), or ESEfinder)
This rule can only be used when splicing predictions models suggest no impact on protein. Do not use protein based computational prediction models for missense variants. BP4

Multiple lines of computational evidence support a deleterious effect on the gene or gene product
At least three in silico splicing predictors in agreement (Human Splicing Finder (HSF), Maximum Entropy (MaxEnt), Berkeley Drosophilia Genome Project (BDGP), or ESEfinder)
Rule code is only for non-canonical splicing variants. Code also does not apply to last nucleotide of exon 3 (c.387G). Do not use protein-based computational prediction models for missense variants. PP3

Null variant in a gene where LoF is a known mechanism of disease
Per ClinGen SVI guidelines PVS1-Supporting

Null variant in a gene where LoF is a known mechanism of disease
Per ClinGen SVI guidelines
Other CDH1 caveats:
G to non G variants disrupting the last nucleotide of an exon
Canonical splice sites located in exons demonstrated experimentally to result in in-frame partial skipping /insertion (e.g., Exon 3 donor site) PVS1-Moderate

Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants.
Per original ACMG/AMP guidelines
No rule specification proposed. Variant example - CDH1 c.2647T>C (Ter883Glnext*29) PM4

Multiple lines of computational evidence support a deleterious effect on the gene or gene product
Variants affecting the same splice site as a well-characterized variant with similar or worse in silico/RNA predictions
Rule code is only for non-canonical splicing variants. Code also does not apply to last nucleotide of exon 3 (c.387G). Do not use protein-based computational prediction models for missense variants. PP3-Moderate

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
Per original ACMG/AMP guidelines
Variant must not impact splicing PS1

Null variant in a gene where LoF is a known mechanism of disease
Per ClinGen SVI guidelines
Other CDH1 caveats:
Use the strong strength of evidence for canonical splice sites
CDH1 Exonic deletions or tandem duplications of in-frame exons
Truncations in NMD-resistant zone located upstream the most 3' well-characterized pathogenic variant c.2506G>T (p.Glu836*). Use PVS1_moderate if premature stop is downstream of this variant PVS1-Strong

Null variant in a gene where LoF is a known mechanism of disease
Per ClinGen SVI guidelines with the exception of canonical splice sites PVS1

Functional Data

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing
Functional RNA studies demonstrating no impact on transcript composition
This rule can only be used to demonstrate lack of splicing and can be downgraded based on quality of dat BS3

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product
RNA assay demonstrating abnormal in-frame transcripts PS3-Supporting

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product
RNA assay demonstrating abnormal out-of-frame transcripts PS3

Segregation Data

Lack of segregation in affected members of a family
Per original ACMG/AMP guidelines
Beware of the presence of phenocopies (e.g., breast cancer) that can mimic lack of segregation. Also, families may have more than one pathogenic variant contributing to another AD disorder BS4

Cosegregation in multiple affected family members in a gene definitively known to cause the disease
Three-four meioses across one or more families PP1

Cosegregation in multiple affected family members in a gene definitively known to cause the disease
Five-six meioses across one or more families PP1-Moderate

Cosegregation in multiple affected family members in a gene definitively known to cause the disease
Seven or more meioses across 2 or more familiess PP1-Strong

De novo Data

Assumed de novo, but w/o confirmation of paternity and maternity
One patient with DGC and/or LBC w/o parental confirmation PM6

Assumed de novo, but w/o confirmation of paternity and maternity
Two or more patients with DGC and/or LBC w/o parental confirmation PM6-Strong

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history
One patient with DGC &/or LBC w/parental confirmation PS2

Assumed de novo, but w/o confirmation of paternity and maternity
Four or more patients with DGC and/or LBC w/o parental confirmation PM6-Very Strong

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history
Two or more patient's with DGC &/or LBC w/ parental confirmation PS2-Very Strong

Allelic Data

Observed in a healthy homozygous individual, or in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant
Variant observed in trans w/known pathogenic variant (phase confirmed) OR observed in the homozygous state in individual w/o personal and/or family history of DGC, LBC, or SRC tumors
Evidence code is dependent on strength of data. Take consideration of quality of sequencing data when applying code. Note that code requires knowledge of individuals' phenotype. Therefore, data from population databases should only be used when phenotypic info is available BP2-Strong

Observed in a healthy homozygous individual, or in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant
Variant is observed in cis (or phase is unknown) w/ a pathogenic variant
Evidence code is dependent on strength of data. Take consideration of quality of sequencing data when applying code. Note that code requires knowledge of individuals' phenotype. Therefore, data from population databases should only be used when phenotypic info is available BP2

Other Data

Variant found in a case with an alternate molecular basis for disease
Per original ACMG/AMP guidelines
This applies if a P/LP variant is identified in an alternate gene known to cause HDGC (e.g., CTNNA1) BP5

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