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 TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 1.0.0

Description : This version specified for the following genes: TP53

Version : 1.0.0

PDF

TP53 VCEP

Released

8/6/2019

14:00:40

Rules for TP53

Gene: TP53 (HGNC:11998) HGNC Name: tumor protein p53 Transcripts: NM_000546.4 Disease: Li-Fraumeni syndrome (MONDO:0007903) Mode of Inheritance: Autosomal dominant 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 Defer to SVI recommendations. Modification Type: Disease-specific,Strength Strong Moderate Supporting 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 Must confirm there is no difference in splicing using RNA data. Can only compare to variants asserted as pathogenic by the ClinGen TP53 EP. This rule code can only be used to compare to variants asserted as pathogenic by the ClinGen TP53 EP. Must confirm there is no difference in splicing using RNA data. Modification Type: Disease-specific,Strength Moderate Must confirm there is no difference in splicing using in silico modeling data. This rule code can be used if there is no difference in splicing using in silico modeling data. This rule code can only be used to compare to variants asserted as pathogenic by the ClinGen TP53 EP. Modification Type: Disease-specific,Strength Supporting 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 SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. >4 points (ex. – 2 cancers in two probands from the strong criteria list or 4 cancers from 4 probands from the moderate criteria). For probands with multiple cancers, use the most specific/highest weight cancer to determine point for that proband. Modification Type: Disease-specific,Strength Strong Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 2-3 points (ex. – 1 cancer from the strong criteria list or 2 from the moderate criteria list) Modification Type: Disease-specific,Strength Moderate Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 1 point (for 1 cancer from the moderate criteria list) Modification Type: Disease-specific,Strength Supporting Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 0.5 point (1 cancer from the moderate criteria list) Modification Type: Disease-specific,Strength Instructions: Apply this code when a de novo variant is identified. The TP53 point system is described below and is based on whether maternity and paternity have been confirmed and the type of cancer(s) seen in the proband. If there are multiple reports of de novo probands, the number of points for each of their cancers are combined. Use the SVI scoring system see below) to determine the strength of the PS2 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 Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that demonstrate a low functioning allele (<20% activity) AND: Evidence of dominant negative effect (DNE) + evidence of LOF from Giacomelli, et al data -OR- There is a 2nd assay showing low function (colony formation assays, apoptosis assays, tetramer assays, knock-in mouse models and growth suppression assays) Modification Type: Disease-specific,Strength Moderate A) Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that demonstrate a partially functioning allele (>20-and <=75% activity) AN Evidence of DNE + evidence of LOF from Giacomelli, et al data. OR There is a 2nd assay showing low function Do not use code with conflicting evidence. B) No transactivation assays (IARC classification based on data Kato et al, 2003) available BUT: Evidence of DNE + evidence of LOF from Giacomelli, et al data. AND There is a 2nd assay showing low function Do not use code with conflicting evidence. Modification Type: Disease-specific,Strength Supporting PS3 Kato et al, 2003 (PMID: 12826609) data performed the best on our test set of variants. These data thus remain the main functional assay underlying the classification. Giacomelli et al, 2018 (PMID: 30224644) assays are systematic and are available for more than 8000 mutants. When using cut-offs derived from original publication data (optimal cut-offs separating silent and common cancer variants), they show good concordance with other ssays. The combination of two assays (DNE + LOF) show better performance than LOF alone (0.88 vs 0.73) and DNE alone (0.88 vs 0.70) when tested on the test set of variants. The performance of DNE+LOF was close to the one of Kato data (0.88 vs 0.94). There are >5900 variants included in Giacomelli dataset (including 378 silent and 414 stopgain variants) that have no Kato data. Over 400 of these variants have at least one entry in the IARC database (somatic). Giacomelli DNE+LOF class can thus be used to support and complement Kato data. Giacomelli DNE+LOF data could be used when there is no Kato data but with a moderate code because of the less robust cut-offs of the assays. Non-systematic assays are harder to interpret but if there are several of them and if all suggest benign or pathogenic, they should be taken into account. A large proportion of these assays is documented in the IARC database and thus be easily found by curators. - Kotler data are available for a large number of mutants, but only for mutants within the DNA binding domain. They will be used as other non-systematic LOF assay. - For variants that are partially functional by Kato, Giacomelli LOF/DNE can be used as results correlate well with Kotler data and quantitative model outputs. Data supporting Functional classes: IARC Transactivation class: IARC classification based on transactivation assays in yeast from Kato et al., (2003): non-functional is <=20% activity; partially functional is >20% and <=75% activity; functional and supertrans are >75% activity. Giacomelli et al. (2018): IARC classification based on growth suppression assays in A549 human cells; DNE+LOF is p53WTNutlin3 Z-score >= 0.61 and Etoposide Z-score <= -0.21; noDNE+noLOF is p53WTNutlin3 Z-score < 0.61 and Etoposide Z-score > -0.21. Other assays (available in IARC database or original publications): in vitro growth assays in H1299 human cells from Kotler et al., (2018) with RFS score >= -1.0 for LOF and RFS score <1 for noLOF; or colony formation assays, growth suppression assays, apoptosis assays, tetramer assays, knock-in mouse models. Modification Type: Disease-specific,Strength Instructions: Kato et al., 2003 (PMID: 12826609) systematic data performed best on our test set of reference variants. These data thus remain the primary functional assay underlying the classification. Giacomelli et al., 2018 (PMID: 30224644) assays are also systematic and are available for all p53 missense variants. When using cut-offs derived from original publication data (optimal cut-offs separating silent and common cancer variants), they show good concordance with other assays. Giacomelli LOF class can thus be used to support and complement Kato data. If Kato data is supported by Kawaguchi et al., 2005 (PMID: 16007150) in the tetramerization domain and tetramerization is affected, this can be used to apply PS3_Supporting. Kotler et al., 2018 (PMID: 29979965) data are available for a large number of variants with different effects, but only for those within the DNA binding domain. They may be used as an additional non-systematic missense LOF assay or for small deletions. Caveat: Do not apply PS3 at any weight for “missense” variants using assays done at the protein level (such as Kato et al. or Giacomelli et al.) if PP3 is applied based on SpliceAI, or if there is any laboratory evidence, including RNA-seq data, of splicing aberration for the genetic variant being assessed. Data Supporting Functional Classes: Kato et al. 2003 (PMID: 12826609) Transactivation Class: Classification based on the median transactivation activity using eight promoters in yeast. Values can be found in the NCI TP53 Database. Non-functional: ≤ 20% activity Partially-functional: >20% and ≤ 75% activity Functional : >75% activity (variants showing supertransactivation are treated as Functional) Giacomelli et al., 2018 (PMID: 30224644): Classification based on results from growth suppression assays in A549 human cells. LOF: Etoposide Z-score ≤ - 0.21 No LOF: Etoposide Z-score > - 0.21 Kawaguchi et al., 2005 (PMID: 16007150): Classification based on the ability to form an oligomer in yeast. Abnormal: Monomer/dimer Normal: Tetramer Other assays: In vitro growth assays in H1299 human cells from Kotler et al., 2018 (PMID: 29979965) with RFS score ≥ - 1.0 for LOF and RFS score < - 1.0 for noLOF. Or colony formation assays, growth suppression assays, apoptosis assays, tetramer assays, or knock-in mouse models. Non-systematic assays are harder to calibrate, but if they meet Brnich et al., 2019 (PMID: 31892348) recommendations for the application of functional evidence and they are in agreement with Kato et al., 2003 , they should be taken into account. A large proportion of these assays are documented in the NCI TP53 database and thus can easily be found by curators. Second assays that may be considered include colony formation assays, apoptosis assays, tetramer assays, knock-in mouse models, and growth suppression assays. This rule should be used and weighted appropriately for variants with functional evidence of loss of function. Follow SVI guidance regarding control numbers for functional studies. Downgrade to PS3_Moderate if PVS1_Strong is applied. Do not apply PS3 at any strength if PVS1 is applied at full strength. See Functional Flowchart for more information and guidance on application of functional rule codes 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 Strong Use proband counting system described below in text. PS4 = 4+ points Modification Type: Disease-specific,Strength Moderate Use proband counting point system described in text below. PS4_moderate = 2-3 points. Modification Type: Disease-specific,Strength Supporting Use proband counting point system described in text below. PS4_Suppporting = 1 point. Modification Type: Disease-specific,Strength Instructions: There are two widely used criteria used for assessing the likelihood of Li-Fraumeni syndrome; with the Chompret criteria being less restrictive. Individuals meeting Chompret criteria have an estimated 20% risk of harboring a pathogenic TP53 variant (Chompret, et al 2001; PMID: 1133239). Members of the TP53 VCEP calculated likelihood ratios for a patient meeting Classic LFS or Chompret criteria using multigene panel testing from Ambry Genetics Laboratory. Our data showed that individuals meeting Chompret criteria had a LR of >2.08 to ≤4.3 and individuals meeting the Classic LFS criteria had a LR of >4.3 to ≤18.7. We recommend using the following point system for determining the weight of PS4 evidence: Proband meeting Chompret criteria = 0.5 point Proband meeting classic LFS criteria = 1 points If by expert opinion, and justified by consideration of internal laboratory data from large scale multigene panel testing, higher point levels may be awarded (2 instead of 1 for a patient meeting classic LFS, 1 instead of 0.5 for a patient meeting Chompret). Please note: This rule code cannot be applied when a variant also meets BA1 or BS1 criteria. 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 This rule can be applied to variants in hot spots (codons 175, 248, 273, 248, 245, 282, 249), but not to variants within functional domains. Use transcript NM_000546.4. Also use rule for variants with >10 somatic observations cancerhotspots.org (v2). Modification Type: Disease-specific,Strength Supporting Instructions: There are several known major hotspots for the TP53 gene. This code can be used for variants within the following codons using canonical transcript NM_000546.4: 175, 245, 248, 249, 273, 282 This code can also be used for germline missense variants seen in cancerhotspots.org (v2) with ≥ 10 somatic occurrences for the same amino acid change. This follows the recommendation from the ClinGen Germline/Somatic Variant Curation Subcommittee (PMID: 30311369). 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 Variant needs to be absent from controls. Modification Type: Disease-specific,General recommendation 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: This rule does not apply to TP53/Li-Fraumeni syndrome.
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 Supporting Not Applicable Comments: This rule should not be used at this time due to limited data.
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 Multiple pathogenic variants (>2) at that residue using the requirements specified below (excluding known hot spots) would be required. Grantham or BLOSUM should be used to compare the variants. New variant must be equal or worse than known pathogenic variant. Splicing should be ruled out. Can only compare to variants asserted as pathogenic by the ClinGen TP53 EP. Modification Type: Disease-specific,Strength Supporting Grantham or BLOSUM should be used to compare variants. The new variant must be equal or worse than known mutation. Splicing should be ruled out. This rule cannot be used for hot spots. Modification Type: Disease-specific,Strength Instructions: This evidence code can be applied when there are >2 pathogenic variants at the same residue (excluding known hot spots – see list above). The other variants must be asserted as pathogenic by the ClinGen TP53 EP. Grantham or BLOSUM should be used to compare the variants. The variant being evaluated must be equal or worse than known mutation. Splicing should be ruled out. 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 SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 2-3 points (ex. – 1 cancer from the strong criteria list or 2 from the moderate criteria list). Modification Type: Strength Moderate Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 1 point (for 1 cancer from the moderate criteria list) Modification Type: Strength Supporting Not Applicable Comments: Combined with PS2. Use PS2 instead of PM6.
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 Cosegregation must be observed in ≥ 7 meioses across > 1 family Modification Type: Disease-specific,Strength Moderate Cosegregation must be observed in 5-6 meioses in 1 family to apply this rule. Modification Type: Disease-specific,Strength Supporting Cosegregation must be observed in 3-4 meioses in 1 family to apply this rule. Modification Type: Disease-specific,Strength 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: This rule should not be used due to the high frequency of benign missense variants.
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 Missense variants (See flowchart for application of PP3 and BP4 rules for missense variants) aGVGD Class C65 and BayesDel score ≥ 0.16 Modification Type: Disease-specific,Strength Supporting PolyPhen2 and SIFT in silico modeling programs should not be used for this gene. Concordance of two predictors is recommended for this gene: Missense variants: aGVGD (Zebrafish; Class C15 and higher are considered evidence of pathogenicity) and BayesDel (scores > 0.16 are considered evidence of pathogenic) Splicing variants: MaxEntScan and HSF Modification Type: Disease-specific,Strength Instructions: PolyPhen2 and SIFT in silico modeling programs should not be used for this gene. Concordance of two predictors is recommended for this gene: Missense variants: according to a published study by Fortuno et al., 2018 comparing the performance of different bioinformatics tools for TP53 (PMID: 29775997), the tools selected are aGVGD (Zebrafish; Class C15 and higher are considered evidence of pathogenicity) and BayesDel (scores > 0.16 are considered evidence of pathogenic). Please refer to the cited manuscript for further details. Splicing variants: MaxEntScan and Human Splicing Finder (HSF) 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 Supporting Not Applicable Comments: 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 Frequency cutoff of 0.1% minimum of 5 alleles present in the population. Use a minor allele frequency cutoff of >0.001 or 0.1% (99.99% CI, sub-population must have a minimum of 5 alleles present in the sub-population) based on the Whiffen-Ware calculator. To set the stand-alone benign MAF cutoff, we used the MAF cutoff established for BS1 (see below) and increased 0.0003 one order of magnitude to come to a value of 0.001. Modification Type: Disease-specific Very Strong Strong Moderate Supporting 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 Frequency cutoff of 0.03%; minimum of 5 alleles present in the population. Use a minor allele frequency cutoff of >0.0003 but <0.001 (99.99% CI, sub-population must have a minimum of 5 alleles present in the sub-population) based on the Whiffen-Ware calculator. To set the strong benign MAF cutoff, we used a prevalence of 1 in 5,000 from Lalloo, et a 2006 (PMID:16644204). We set the genetic and allelic heterogeneity at 100% and penetrance at 30%. Modification Type: Disease-specific Moderate Supporting 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 Observed in >8 cancer free 60+ year old females. Modification Type: Disease-specific Moderate Supporting Observed in 2-7 cancer free 60+ year old females. Modification Type: Disease-specific Instructions: Using TP53 multigene panel testing results from two diagnostic labs, we compared the proportion of cancer-free individuals by age 60 in TP53 carriers versus TP53-negative controls. Based on the correspondence between likelihood ratios of pathogenicity and different levels of strengths for ACMG/AMP rules in the study by Tavtigian et al., 2018 (PMID: 29300386), our most conservative results support the following: - BS2 – This evidence code can be used when a variant is observed in >8 cancer free 60+ year old females. - BS2_Supporting – This evidence code can be used when a variant is observed in 2-7 cancer free 60+ year old females. 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 Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that show retained function (76-140% activity) or supertransactivation function AND: No evidence of DNE + no evidence of LOF from Giacomelli, et al data. -OR- There is a 2nd assay, including colony formation assays, apoptosis assays, tetramer assays, growth suppression and knock-in mouse models demonstrating retained function. Modification Type: Disease-specific,Strength Moderate Supporting Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that demonstrate a partially functioning allele (>20% and <=75% activity) AND: No evidence of DNE + no evidence of LOF from Giacomelli, et al data. OR There is a 2nd assay demonstrating retained function. Do not use code with conflicting evidence. No transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) available BUT: No evidence of DNE + no evidence of LOF from Giacomelli, et al data. AND There is a 2nd assay showing retained function Do not use code with conflicting evidence Modification Type: Disease-specific,Strength 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 Variant segregates to opposite side of the family who meets LFS criteria OR Variant is present in ≥3 living unaffected individuals (at least 2 of 3 should be female) above 55 years of age. Modification Type: Disease-specific 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: This rule code does not apply to these genes, as truncating variants account for only a portion of disease causing variants.
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 Variant is observed in trans with a pathogenic or likely pathogenic TP53 variant (phase confirmed) OR 3 or more observations when phase is unknown with at least two different pathogenic/likely pathogenic TP53 variants Modification Type: Disease-specific Instructions: This evidence code can be applied in either scenario below: Variant is observed in trans with a pathogenic or likely pathogenic TP53 variant (phase confirmed). When there are 3 or more observations with a pathogenic or likely pathogenic variant when phase is unknown. In this scenario, the variant must be seen with at least two different pathogenic/likely pathogenic TP53 variants. Not Applicable Comments: 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: Not applicable
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 Missense: aGVGD (zebrafish; Class C0 or C15 is considered evidence of non-pathogenicity) and BayesDel <0.16 is considered evidence on non-pathogenicity Splicing: MaxEntScan and HSF Modification Type: Disease-specific,Strength Instructions: PolyPhen2 and SIFT in silico modeling programs should not be used for this gene. Concordance of two predictors is recommended for this gene: Missense variants: according to a published study by Fortuno et al., 2018 comparing the performance of different bioinformatics tools for TP53 (PMID: 29775997), the tools selected are aGVGD (Zebrafish; Class C0 or C15 is considered evidence of non-pathogenicity) and BayesDel <0.16 is considered evidence on non-pathogenicity Splicing variants: MaxEntScan and Human Splicing Finder (HSF) 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 Not Applicable Comments: 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 Concordance of MaxEntScan and HSF; If a new alternate site is predicted, compare strength to native site in interpretation. Modification Type: Disease-specific Not Applicable

Rules for Combining Criteria

Pathogenic

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

1 Very Strong (PVS1, PS2_Very Strong) AND ≥ 2 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate)

1 Very Strong (PVS1, PS2_Very Strong) AND 1 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate) AND 1 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

1 Very Strong (PVS1, PS2_Very Strong) AND ≥ 2 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

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

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

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 2 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate) AND ≥ 2 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 1 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate) AND ≥ 4 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

Likely Pathogenic

1 Very Strong (PVS1, PS2_Very Strong) AND 1 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 1 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND ≥ 2 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

≥ 3 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate)

2 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate) AND ≥ 2 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

1 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate) AND ≥ 4 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 2 Moderate (PS1_Moderate, PS2_Moderate, PS3_Moderate, PS4_Moderate, PM1, PM5, PM6, PP1_Moderate, PP3_Moderate)

1 Very Strong (PVS1, PS2_Very Strong) AND 1 Supporting (PS2_Supporting, PS3_Supporting, PS4_Supporting, PM2_Supporting, PM5_Supporting, PP1, PP3)

Benign

≥ 2 Strong (BS1, BS2, BS3, BS4)

1 Stand Alone (BA1)

Likely Benign

1 Strong (BS1, BS2, BS3, BS4) AND 1 Supporting (BS2_Supporting, BS3_Supporting, BP2, BP4, BP7)

≥ 2 Supporting (BS2_Supporting, BS3_Supporting, BP2, BP4, BP7)