Criteria Specification Registry

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Criteria Specification

ClinGen Coagulation Factor Deficiency Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for F9 Version 1.0.0

Description : Rule specifications for hemophilia B.

Version : 1.0.0 Release Notes :

Edits post SVI review

Coagulation Factor Deficiency VCEP

Released

10/5/2023

13:25:41

Rules for F9

Gene: F9 (HGNC:3551) HGNC Name: coagulation factor IX Transcripts: NM_000133.4 Disease: hemophilia B (MONDO:0010604) Mode of Inheritance: X-linked inheritance

Criteria & Strength Specifications
PVS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease. Caveats: • Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7). • Use caution interpreting LOF variants at the extreme 3’ end of a gene. • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact. • Use caution in the presence of multiple transcripts. Stand Alone Very Strong Per Coagulation Factor Deficiency VCEP/SVI PVS1 decision tree. Modification Type: Gene-specific Strong Per Coagulation Factor Deficiency VCEP/SVI PVS1 decision tree. Modification Type: Gene-specific Moderate Per Coagulation Factor Deficiency VCEP/SVI PVS1 decision tree. Modification Type: Gene-specific Supporting Per Coagulation Factor Deficiency VCEP/SVI PVS1 decision tree. Modification Type: Gene-specific Instructions: Apply the ClinGen Coagulation Factor Deficiency VCEP/SVI decision tree to determine use and strength of the PVS1 rule. Not Applicable
PS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Example: Val->Leu caused by either G>C or G>T in the same codon. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. Stand Alone Very Strong Strong This evidence code can be applied when there is 1 pathogenic variant or 2 likely pathogenic variants at the same residue based on F9 gene rule specifications from the Coagulation Factor Deficiency VCEP and where in silico predictors do not suggest a splicing defect. Modification Type: General recommendation Moderate This evidence code can be applied when there is 1 likely pathogenic variants at the same residue based on F9 gene rule specifications from the Coagulation Factor Deficiency VCEP and where in silico predictors do not suggest a splicing defect. Modification Type: General recommendation Supporting Not Applicable Comments: Not applicable for CDH1.
PS2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity. Stand Alone Very Strong Use the SVI recommendations for de novo cases; 4 points. Use de novo guidance below to determine point value. Modification Type: Disease-specific Strong Use the SVI recommendations for de novo cases; 2 points. Use de novo guidance below to determine point value. Modification Type: Disease-specific Moderate Use the SVI recommendations for de novo cases; 1 point. Use de novo guidance below to determine point value. Modification Type: Disease-specific Supporting Use the SVI recommendations for de novo cases; 0.5 point. Use de novo guidance below to determine point value. Modification Type: Disease-specific Instructions: Use ClinGen’s de novo modified point system for a highly specific phenotype (see guidance below). Combine all assumed and confirmed de novo cases for this code and use at the appropriate strength based on amount of points for all probands. Probands must meet the PS4 phenotype criteria to apply this code. Not Applicable
PS3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established. Stand Alone Very Strong Strong Abnormal factor IX activity level (<40 IU/dL or 40%) in a cell line and/or mouse model. Modification Type: Disease-specific Moderate Abnormal factor IX activity level (<40 IU/dL or 40%) studied in an animal model setting other than mouse (i.e. – bovine factor IX activity levels compared to factor X levels). Modification Type: Disease-specific Supporting Absent or significantly reduced factor IX antigen level compared to wildtype using conformation-specific reporter assay in cell lines. Modification Type: Disease-specific Instructions: See functional study spreadsheet. Not Applicable
PS4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence. Stand Alone Very Strong ≥8 probands meet criteria described below Modification Type: Disease-specific Strong 4-7 probands meet criteria described below Modification Type: Disease-specific Moderate 2-3 probands meet criteria described below Modification Type: Disease-specific Supporting 1 proband meets criteria described below Modification Type: Disease-specific Instructions: Hemophilia B phenotype requirements: -Abnormal factor IX activity levels in the severe, moderate or mild range (< 40% factor IX activity level) are sufficient to confer a diagnosis. -Variants associated with moderate or severe disease should be absent in gnomAD or other population databases. However, variants associated with mild disease severity can be observed in up to 3 males in population databases, as long as the number of probands would qualify this code to be used at a very strong weight. Variants associated with mild disease severity with 1-2 alleles in population databases must qualify this code to be used at a strong weight. Not Applicable
PM1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation. Stand Alone Very Strong Strong This code can be used for variants affecting any of the 3 catalytic residues (H267, D315 or S411) and 2 activation residues (R191-A192 and R226-V227) in the F9 gene (PMID: 12554099). Modification Type: Gene-specific Moderate This code should be applied when the variant is within exons 3, 4 or 5. Modification Type: Gene-specific Supporting Instructions: The combined weight of codes PM1 and PM5 applied for a single variant can only equal strong. Not Applicable Comments: Not applicable for CDH1.
PM2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Caveat: Population data for indels may be poorly called by next generation sequencing. Stand Alone Very Strong Strong Moderate Supporting Variant must be absent in males in population databases, such as gnomAD. Modification Type: Disease-specific Instructions: none Not Applicable
PM3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary For recessive disorders, detected in trans with a pathogenic variant Note: This requires testing of parents (or offspring) to determine phase. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: Not applicable for the F9 gene.
PM4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Stand Alone Very Strong Strong Moderate Use code with no specification. Modification Type: None Supporting Instructions: . Not Applicable
PM5 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. Example: Arg156His is pathogenic; now you observe Arg156Cys. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. Stand Alone Very Strong Strong Moderate This evidence code can be applied when there is 1 pathogenic variant or 2 likely pathogenic variants at the same residue based on F9 rule specification from the Coagulation Factor Deficiency VCEP and where in silico predictors do not suggest a splicing defect. Modification Type: Gene-specific Supporting This evidence code can be applied when there is 1 likely pathogenic variant at the same residue based on F9 rule specifications Coagulation Factor Deficiency VCEP and where in silico predictors do not suggest a splicing defect. A “highly suspicious” VUS is defined as a variant that is 1 supporting code away from reaching a likely pathogenic classification. Modification Type: Gene-specific Instructions: The combined weight of codes PM1 and PM5 applied for a single variant can only equal strong. Not Applicable
PM6 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Assumed de novo, but without confirmation of paternity and maternity. Stand Alone Very Strong Strong Moderate Supporting Instructions: Use ClinGen’s de novo point system for a highly specific phenotype. Not Applicable Comments: This rule code is combined with PS2. Please combined assumed de novo cases with confirmed de novo cases and apply PS2 at the appropriate weight.
PP1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. Note: May be used as stronger evidence with increasing segregation data. Stand Alone Very Strong Strong This code is applicable when there ≥4 meioses across ≥2 families. Modification Type: Disease-specific Moderate This code is applicable when there are at least 3 meioses across one or more families. Modification Type: Disease-specific Supporting This code is applicable when there 2 meioses in one family OR 1 meiosis between 2 affected siblings. Modification Type: Disease-specific Instructions: Base strength of rule code on number of meioses across one or more families. Not Applicable
PP2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: Not applicable for F9.
PP3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant. Stand Alone Very Strong Strong Moderate Supporting Code can be applied for variants where the REVEL score is greater than or equal to 0.6 or a SpliceAI score of greater than or equal to 0.5. Modification Type: Gene-specific Instructions: none Not Applicable
PP4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. Stand Alone Very Strong Strong Moderate Proband must meet hemophilia B phenotype criteria AND have full gene sequencing and deletion/duplication analysis. Modification Type: Disease-specific Supporting Instructions: Hemophilia B phenotype requirements: -Abnormal factor IX activity levels in the severe, moderate or mild range (< 40% factor IX activity level) are sufficient to confer a diagnosis. -A proband must have had full gene sequencing and deletion/duplication analysis to apply this code. -A proband used for this code cannot be applied towards the PS4 count. Not Applicable Comments: Use PS4 to count probands with hemophilia B diagnosis.
PP5
Original ACMG Summary Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation. Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BA1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Stand Alone MAF cutoff of greater than or equal to 0.0000556 (or 0.00556%). Modification Type: Gene-specific Very Strong Strong Moderate Supporting Instructions: 99.99% CI; subpopulation must have a minimum of five variant alleles present. Males and females are included for this code. Not Applicable
BS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Allele frequency is greater than expected for disorder. Stand Alone Very Strong Strong MAF cutoff of greater than or equal to 0.00000556 (or 0.000556%). Modification Type: Gene-specific Moderate Supporting Instructions: 99.99% CI; subpopulation must have a minimum of five variant alleles present. Males and females are included for this code. Not Applicable
BS2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. Stand Alone Very Strong Strong This evidence code can be used when a F9 variant is observed in a male with a normal factor IX activity level (<40% IU). Modification Type: Disease-specific Moderate Supporting Instructions: none Not Applicable
BS3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing. Stand Alone Very Strong Strong This code can be used for F9 gene variants studied in a cell line or mouse model setting that confer a normal factor IX activity AND normal factor IX antigen levels OR normal Western Blot. Modification Type: Disease-specific Moderate Supporting Instructions: none Not Applicable
BS4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Lack of segregation in affected members of a family. Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation. Stand Alone Very Strong Strong This evidence code can be used when a F9 variant is observed in a male with a family history of hemophilia B and has a normal factor IX activity level. Modification Type: Disease-specific Moderate Supporting Instructions: none Not Applicable
BP1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Missense variant in a gene for which primarily truncating variants are known to cause disease. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: Not applicable for F9 gene.
BP2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern. Stand Alone Very Strong Strong Moderate Supporting Instructions: Evidence code is dependent on the strength of data. Take consideration of the quality of sequencing data when applying code. Not Applicable Comments: Not being used at this time. There are reports of males with hemophilia having two suspicious pathogenic variants.
BP3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary In frame-deletions/insertions in a repetitive region without a known function. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: Not applicable for F9 gene.
BP4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant. Stand Alone Very Strong Strong Moderate Supporting This code can be applied for variants reaching a REVEL score of 0.3 or below AND a Splice AI score of less than or equal to 0.01. Modification Type: Gene-specific Instructions: none Not Applicable
BP5 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Variant found in a case with an alternate molecular basis for disease. Stand Alone Very Strong Strong Moderate Supporting Instructions: This applies if a P/LP variant is identified in an alternate gene known to cause HDGC (currently only CTNNA1). Not Applicable Comments: This rule code is not recommended for use at this time. There is no known alternate cause of isolated factor IX deficiency.
BP6
Original ACMG Summary Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation. Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BP7 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary A synonymous variant for 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. Stand Alone Very Strong Strong Moderate Supporting Splicing prediction score of less than or equal to 0.01 is required. Conservation should be assess using PhyloP (cutoff less than 0.1) and PhastCons (cutoff less than 0.5). Modification Type: Gene-specific Instructions: This code can also be used for non-canonical intronic variants. The use of BP7 with BP4 is allowed, as appropriate, to classify variants meeting both criteria as likely benign. Not Applicable

Rules for Combining Criteria

Pathogenic

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong) AND ≥ 1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM1_Strong, PP1_Strong)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong) AND ≥ 2 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM4, PM5, PP1_Moderate)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong) AND 1 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM4, PM5, PP1_Moderate) AND 1 Supporting (PVS1_Supporting, PS2_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong) AND ≥ 2 Supporting (PVS1_Supporting, PS2_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

≥ 2 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM1_Strong, PP1_Strong)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM1_Strong, PP1_Strong) AND ≥ 3 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM4, PM5, PP1_Moderate)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM1_Strong, PP1_Strong) AND 2 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM4, PM5, PP1_Moderate) AND ≥ 2 Supporting (PVS1_Supporting, PS2_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM1_Strong, PP1_Strong) AND 1 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM4, PM5, PP1_Moderate) AND ≥ 4 Supporting (PVS1_Supporting, PS2_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

Likely Pathogenic

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong) AND 1 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM4, PM5, PP1_Moderate)

Benign

≥ 2 Strong (BS1, BS2, BS3, BS4)

1 Stand Alone (BA1)

Likely Benign

1 Strong (BS1, BS2, BS3, BS4) AND 1 Supporting (BP4, BP7)

≥ 2 Supporting (BP4, BP7)

Files & Images

Pilot Study Results for F8 and F9: Pilot study results for the F8 and F9 rule specifications. Use the tab at the bottom of the spreadsheet to toggle between results for hemophilia A and B.

Guidance for Combined De Novo Rule Code (PS2/PM6): Use this for guidance to apply the combined de novo rule code (PS2/PM6) for hemophilia A or B.

Rule Guidance for Combining Pathogenic and Benign Codes: A point counting policy is used for variants where pathogenic and benign rule codes can be applied rather than defaulting to a VUS classification. This document illustrates how to combine pathogenic and benign rule codes.

F9 Functional Assays: List of approved function assays for F9 variants.

F9 PVS1 Decision Tree: Use this decision tree for variants that fall under the PVS1 umbrella.