Criteria Specification Registry

Criteria Specification (CSpec) Registry is intended to provide access to the Criteria Specifications used and applied by ClinGen Variant Curation Expert Panels and biocurators in the classification of variants.

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Criteria Specification

ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for FOXN1 Version 1.0.0

Version : 1.0.0

Severe Combined Immunodeficiency Disease VCEP

Released

7/29/2024

16:21:55

Rules for FOXN1

All observations of FOXN1 variants may be curated under this single set of specifications and classified for T-cell immunodeficiency, congenital alopecia, and nail dystrophy with semidominant inheritance.

Gene: FOXN1 (HGNC:12765) HGNC Name: forkhead box N1 Transcripts: NM_001369369.1 Disease: T-cell immunodeficiency, congenital alopecia, and nail dystrophy (MONDO:0011132) Mode of Inheritance: Semidominant 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 Use ClinGen SVI recommendations for loss of function criterion (Tayoun et al., 2018 (PMID: 30192042)) with one specification: PVS1 can be applied to variants not predicted to undergo nonsense-mediated decay but removing/altering the critical forkhead domain (amino acids 270-367; Newman et al., 2020; PMID: 31914405) based on recommendations from Walker et. al., 2023 (PMID: 37352859). Modification Type: General recommendation,Gene-specific Strong Use ClinGen SVI recommendations for loss of function criterion (Tayoun et al., 2018 (PMID: 30192042)) with two specifications: For variants not predicted to undergo nonsense-mediated decay, but removing >10% of protein, (i.e. variants in the last exon, exon 9, or variants in the last 50 nucleotides of the penultimate exon after c.1577, codon 526, in exon 8), at least one pathogenic variant must be present downstream in order to apply PVS1_Strong PVS1_Strong can be applied to variants not predicted to undergo nonsense-mediated decay but removing/altering the transactivation domain (amino acids 511-563; Schlake et al., 2000 PMID: 10767081). Modification Type: General recommendation,Gene-specific Moderate Use ClinGen SVI recommendations for loss of function criterion (Tayoun et al., 2018 (PMID: 30192042)) with one specification: For variants not predicted to undergo nonsense-mediated decay, but removing >10% of protein, (i.e. variants in the last exon, exon 9, or variants in the last 50 nucleotides of the penultimate exon after c.1577, codon 526, in exon 8), when at least one pathogenic variant is not present downstream downgrade to PVS1_Moderate Modification Type: General recommendation Supporting Instructions: See attached PVS1 flowchart. 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 Applicable for a same amino acid change if previously established variant is classified as pathogenic by SCID VCEP specifications for FOXN1. Can also be applied for variants with the same predicted splicing event as a known Pathogenic variant (as classified by the SCID VCEP specifications for FOXN1), only when the strength of the prediction for the variant under assessment is of similar or higher strength than the strength of the prediction for the comparison (Likely) Pathogenic variant (i.e., per in silico splicing tool SpliceAI). See attached instructions (from Table 2 of PMID: 37352859) for determining when PS1 should be applied at PS1_Strong, _Moderate, or _Supporting. Modification Type: Gene-specific Moderate Applicable for a same amino acid change if previously established variant is classified as likely pathogenic by SCID VCEP specifications for FOXN1. Can also be applied for variants with the same predicted splicing event as a known (Likely) Pathogenic variant (as classified by the SCID VCEP specifications for FOXN1), only when the strength of the prediction for the variant under assessment is of similar or higher strength than the strength of the prediction for the comparison (Likely) Pathogenic variant (i.e., per in silico splicing tool SpliceAI). See attached instructions (from Table 2 of PMID: 37352859) for determining when PS1 should be applied at PS1_Strong, _Moderate, or _Supporting. Modification Type: Gene-specific,Strength Supporting Can be applied for variants with the same predicted splicing event as a known (Likely) Pathogenic variant (as classified by the SCID VCEP specifications for FOXN1), only when the strength of the prediction for the variant under assessment is of similar or higher strength than the strength of the prediction for the comparison (Likely) Pathogenic variant (i.e., per in silico splicing tool SpliceAI). See attached instructions (from Table 2 of PMID: 37352859) for determining when PS1 should be applied at PS1_Strong, _Moderate, or _Supporting. Modification Type: Gene-specific,Strength Not Applicable
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 ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Strong Use ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Moderate Use ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Supporting Use ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Instructions: See attached scoring guide. The following guidelines should be used when determining phenotypic consistency of each proband: “Phenotype highly specific for gene” proband must meet PP4_Moderate criteria “Phenotype consistent with gene but not highly specific” proband must meet PP4 criteria “Phenotype consistent with gene but not highly specific and high genetic heterogeneity” proband does not meet PP4 criteria but has at least one of three core FOXN1 deficiency features (Congenital alopecia, Nail dystrophy, T lymphopenia) 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 PS3 may be applied at the strong level for evidence from an animal model expressing the variant of interest and recapitulating FOXN1 deficiency (i.e. a mouse model with T cell lymphopenia). Modification Type: Gene-specific Moderate PS3 may be applied at the moderate level based on a luciferase assay showing reduced (<50%) activity, as part of a validated assay with pathogenic and benign controls (PMID: 37419334). Modification Type: Gene-specific,Strength Supporting PS3 may be applied at the supporting level based on a luciferase assay, without sufficient validation controls, showing reduced (<50%) activity, such as those reported in PMIDs: 31566583, 33464451, 34860543. Modification Type: Gene-specific,Strength 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 Sum of case scores ≥8 points (see instructions below) Modification Type: Disease-specific Strong Sum of case scores 4-7.75 points (see instructions below) Modification Type: Disease-specific Moderate Sum of case scores 2-3.75 points (see instructions below) Modification Type: Disease-specific Supporting Sum of case scores 1-1.75 points (see instructions below) Modification Type: Disease-specific Instructions: Evaluate each unrelated heterozygous affected individual with the attached Affected Observations Scoring Guide and sum points across all probands. Exclude the proband used to satisfy the PP4 criteria Caveat: variant must be sufficiently rare (meet PM2_supporting specification). 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 Moderate Applicable for variants in the DNA binding forkhead domain (amino acids 270-367), which is a well-established functional domain (Newman et al., 2020; PMID: 31914405) of FOXN1 with low tolerance for benign variation. Modification Type: Gene-specific Supporting Not Applicable
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 gnomAD Grpmax filtering allele frequency ≤0.00002412 Modification Type: Gene-specific Instructions: This value is based on the HMAF of NM_001369369.1(FOXN1):c.1585del (p.Leu529fs), the most common pLOF variant present in gnomADv4.0.0 that classifies as Pathogenic based on specified guidelines. 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 Sum of case scores ≥8 points (see instructions below) Modification Type: General recommendation Strong Sum of case scores 4-7.75 points (see instructions below) Modification Type: General recommendation Moderate Sum of case scores 2-3.75 points (see instructions below) Modification Type: General recommendation Supporting Sum of case scores 1-1.75 points (see instructions below) Modification Type: General recommendation Instructions: Evaluate each unrelated homozygous or compound heterozygous affected individual with the attached Affected Observations Scoring Guide and sum points across all probands. Caveat: additional requirement that the co-occurring variant must be classified using the SCID VCEP specifications for FOXN1. Caveat: variants must be sufficiently rare (meet PM2_supporting specification). Not Applicable
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 Additional requirement that when applied to deletion variants, the deleted region must contain a known pathogenic or likely pathogenic variant that is not predicted/observed to alter splicing. Modification Type: Gene-specific Supporting Additional requirement that when applied to deletion variants, the deleted region must contain a known VUS variant that is not predicted/observed to alter splicing. Modification Type: Gene-specific,Strength 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 Applicable if previously established variant is classified as pathogenic by SCID VCEP specifications for FOXN1. Previously established variant must be classified by SCID VCEP specifications for FOXN1. Modification Type: Gene-specific Supporting Applicable if previously established variant is classified as likely pathogenic by SCID VCEP specifications for FOXN1. Previously established variant must be classified by SCID VCEP specifications for FOXN1. Modification Type: Gene-specific,Strength 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 Use ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Moderate Use ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Supporting Use ClinGen SVI recommendations for de novo criteria (see instructions below). Modification Type: General recommendation,Gene-specific Instructions: See attached scoring guide. The following guidelines should be used when determining phenotypic consistency of each proband: “Phenotype highly specific for gene” proband must meet PP4_Moderate criteria “Phenotype consistent with gene but not highly specific” proband must meet PP4 criteria “Phenotype consistent with gene but not highly specific and high genetic heterogeneity” proband does not meet PP4 criteria but has at least one of three core FOXN1 deficiency features (Congenital alopecia, Nail dystrophy, T lymphopenia) Not Applicable
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 Can be applied when there is a 32:1 likelihood ratio (LOD score ≥1.5, summed across all families with segregation evidence) per recommendations from PMID: 30311386 Table 4a. See instructions for calculating the estimated LOD score. Modification Type: General recommendation Moderate Can be applied when there is a 16:1 likelihood ratio (LOD score 1.2-<1.5, summed across all families with segregation evidence) per recommendations from PMID: 30311386 Table 4a. See instructions for calculating the estimated LOD score. Modification Type: General recommendation Supporting Can be applied when there is a 4:1 likelihood ratio (LOD score 0.6-<1.2, summed across all families with segregation evidence) per recommendations from PMID: 30311386 Table 4a. See instructions for calculating the estimated LOD score. Modification Type: General recommendation Instructions: The estimated LOD (Z) score is calculated as follows Z = log₁₀ {1/[(0.25)^x(0.5)^y]} x is the number of affected relatives with at least one core feature (see top three bullet/sub-bullet points of PP4) harboring biallelic FOXN1 variants (confirmed by genetic analysis), not including the proband y is the number of affected relatives with at least one core feature (see top three bullet/sub-bullet points of PP4) harboring a heterozygous FOXN1 variant (confirmed by genetic analysis or an obligate carrier), not including the proband 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: Does not apply, FOXN1 does not have a low rate of benign missense variation, with a missense constraint score of Z=0.66.
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 Moderate evidence can be applied for a REVEL score of ≥0.932, downgraded from the recommendation of Strong in Pejaver et al., 2022 (PMID: 36413997). Modification Type: General recommendation Supporting Supporting evidence can be applied for a REVEL score of ≥0.644 (to <0.932), based on recommendations of Pejaver et al., 2022 (PMID: 36413997). Also applicable to missense, synonymous, or intronic variants predicted to impact splicing by SpliceAI ∆ score ≥0.2 Modification Type: General recommendation 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 Patient score of ≥2 points (see instructions below) Modification Type: Disease-specific,Gene-specific Supporting Patient score of 1-<2 points (see instructions below) Modification Type: Disease-specific,Gene-specific Instructions: PP4 applicability and strength is determined by the total points accumulated by a single affected individual according to the list below: Core Features Congenital, or early-onset, alopecia or absent eyebrows (0.25pt) Nail dystrophy (0.25pt) Absent/very low T cell number of <0.05x10^9/L (0.5pt) OR if >0.05x10^9/L then: Low T cell number for age 0.05-1.0x10^9/L OR T- B+ [NK+]* SCID OR Poor/absent proliferative response to phytohemagglutinin (PHA) (0.25pt) Abnormal TRECs OR <20% of CD4+ T cells are naïve (naïve T cells should be measured via CD3/CD4/CD45RA, or with additional naive markers) OR low CD8+ T cell number relative to age-matched controls (0.25pt) Additional Features Development of T cells in an artificial thymic organoid (ATO) system (0.25pt) Transplant of thymic tissue corrects T cell deficiency (0.5pt) SCID gene panel or exome/genome sequencing (0.5pt), with no other variant of interest reported *Absent NK cells would not be consistent with a FOXN1 specific phenotype, however if absence/presence of NK cells is not noted, points may still be awarded if SCID gene panel or exome/genome sequencing has ruled out alternative causes Not Applicable
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 gnomAD Grpmax filtering allele frequency >0.00447 Modification Type: Gene-specific Very Strong Strong Moderate Supporting Instructions: Maximum credible population allele frequency threshold determined using Whiffin/Ware calculator (https://www.cardiodb.org/allelefrequencyapp/) and the following parameters: Prevalence: 1:5,000 Allelic heterogeneity: 1 Genetic heterogeneity: 0.01 Penetrance: 10% 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 gnomAD Grpmax filtering allele frequency >0.00141 OR a bottle-necked population with a MAF >0.00141 may be used for this criterion. Caveat: If the variant is known to be a founder variant in the bottle-necked population do not consider the frequency in that population for BS1. Modification Type: Gene-specific Moderate Supporting Instructions: Maximum credible population allele frequency threshold determined using Whiffin/Ware calculator (https://www.cardiodb.org/allelefrequencyapp/) and the following parameters: Prevalence: 1:50,000 Allelic heterogeneity: 1 Genetic heterogeneity: 0.01 Penetrance: 10% 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 Moderate Supporting Not Applicable Comments: Does not apply due to reduced penetrance.
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 Moderate Supporting Not Applicable Comments: There is not a well-established functional study which can rule out all damaging effects on protein function.
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 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. Modification Type: None Moderate Supporting 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: Does not apply.
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 Applicable only when observed in cis with a pathogenic variant in any inheritance pattern, with the additional requirement that the co-occurring variant must be classified using the SCID VCEP specifications for FOXN1. Modification Type: Disease-specific Not Applicable
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: Does not apply.
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 •Supporting evidence can be applied for a REVEL score of <0.290 based on recommendations of Pejaver et al., 2022 (PMID: 36413997). •Also applicable to synonymous or intronic variants not predicted to impact splicing by SpliceAI ∆ score ≤0.1 Modification Type: General recommendation 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 Use with no specification. Modification Type: None Not Applicable
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 A synonymous variant, or deep intronic variant affecting nucleotides at or beyond the +7 (donor) and -21 (acceptor) positions, for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site (SpliceAI ∆ score ≤0.1) AND the nucleotide is not highly conserved. Modification Type: General recommendation Not Applicable

Rules for Combining Criteria

Pathogenic

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM3_Very Strong) AND ≥ 1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM3_Strong, PM6_Strong, PP1_Strong)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM3_Very Strong) AND ≥ 2 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM3_Very Strong) AND 1 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate) AND 1 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM3_Very Strong) AND ≥ 2 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

≥ 2 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM3_Strong, PM6_Strong, PP1_Strong)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM3_Strong, PM6_Strong, PP1_Strong) AND ≥ 3 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM3_Strong, PM6_Strong, PP1_Strong) AND 2 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate) AND ≥ 2 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM3_Strong, PM6_Strong, PP1_Strong) AND 1 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate) AND ≥ 4 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

Likely Pathogenic

1 Strong (PVS1_Strong, PS1, PS2, PS3, PS4, PM3_Strong, PM6_Strong, PP1_Strong) AND ≥ 2 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

≥ 3 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate)

2 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate) AND ≥ 2 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

1 Moderate (PVS1_Moderate, PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM3, PM4, PM5, PM6, PP1_Moderate, PP3_Moderate, PP4_Moderate) AND ≥ 4 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM3_Very Strong) AND 1 Supporting (PS1_Supporting, PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM3_Supporting, PM4_Supporting, PM5_Supporting, PM6_Supporting, PP1, PP3, PP4)

Benign

≥ 2 Strong (BS1, BS4)

1 Stand Alone (BA1)

Likely Benign

1 Strong (BS1, BS4) AND 1 Supporting (BP2, BP4, BP5, BP7)

≥ 2 Supporting (BP2, BP4, BP5, BP7)

Files & Images

PS2_PM6: SVI recommendations for de novo criteria

PS4_PM3: Affected Observations Scoring Guide

PS3: Approved assays

PVS1 flowchart:

PS1_Splice: SVI recommendations for application of PS1 to variants impacting splicing