owencqueen/cgbench_data huggingface dataset:
Gene: TP53 (HGNC:11998)
Evidence Code: PVS1 — Very Strong
Modification Type: Disease-specific,Strength
Defer to SVI recommendations.
Gene: TP53 (HGNC:11998)
Evidence Code: PS1 — Strong
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PS1 — Moderate
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PS2 — Very Strong
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PS2 — Strong
Modification Type: Disease-specific,Strength
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)
Gene: TP53 (HGNC:11998)
Evidence Code: PS2 — Moderate
Modification Type: Disease-specific,Strength
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)
Gene: TP53 (HGNC:11998)
Evidence Code: PS2 — Supporting
Modification Type: Disease-specific,Strength
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)
Gene: TP53 (HGNC:11998)
Evidence Code: PS3 — Strong
Modification Type: Disease-specific,Strength
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)
Gene: TP53 (HGNC:11998)
Evidence Code: PS3 — Moderate
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PS3 — Supporting
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PS4 — Strong
Modification Type: Disease-specific,Strength
Use proband counting system described below in text.
PS4 = 4+ points
Gene: TP53 (HGNC:11998)
Evidence Code: PS4 — Moderate
Modification Type: Disease-specific,Strength
Use proband counting point system described in text below.
PS4_moderate = 2-3 points.
Gene: TP53 (HGNC:11998)
Evidence Code: PS4 — Supporting
Modification Type: Disease-specific,Strength
Use proband counting point system described in text below.
PS4_Suppporting = 1 point.
Gene: TP53 (HGNC:11998)
Evidence Code: PM1 — Moderate
Modification Type: Disease-specific,Strength
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).
Gene: TP53 (HGNC:11998)
Evidence Code: PM2 — Supporting
Modification Type: Disease-specific,General recommendation
Variant needs to be absent from controls.
Gene: TP53 (HGNC:11998)
Evidence Code: PM5 — Moderate
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PM5 — Supporting
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: PM6 — Strong
Modification Type: Strength
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).
Gene: TP53 (HGNC:11998)
Evidence Code: PM6 — Moderate
Modification Type: Strength
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)
Gene: TP53 (HGNC:11998)
Evidence Code: PP1 — Strong
Modification Type: Disease-specific,Strength
Cosegregation must be observed in ≥ 7 meioses across > 1 family
Gene: TP53 (HGNC:11998)
Evidence Code: PP1 — Moderate
Modification Type: Disease-specific,Strength
Cosegregation must be observed in 5-6 meioses in 1 family to apply this rule.
Gene: TP53 (HGNC:11998)
Evidence Code: PP1 — Supporting
Modification Type: Disease-specific,Strength
Cosegregation must be observed in 3-4 meioses in 1 family to apply this rule.
Gene: TP53 (HGNC:11998)
Evidence Code: PP3 — Moderate
Modification Type: Disease-specific,Strength
Missense variants
 
(See flowchart for application of PP3 and BP4 rules for missense variants)


aGVGD Class C65 and BayesDel score ≥ 0.16
Gene: TP53 (HGNC:11998)
Evidence Code: PP3 — Supporting
Modification Type: Disease-specific,Strength
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
Gene: TP53 (HGNC:11998)
Evidence Code: BA1 — Stand Alone
Modification Type: Disease-specific
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.
Gene: TP53 (HGNC:11998)
Evidence Code: BS1 — Strong
Modification Type: Disease-specific
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%.
Gene: TP53 (HGNC:11998)
Evidence Code: BS2 — Strong
Modification Type: Disease-specific
Observed in >8 cancer free 60+ year old females.
Gene: TP53 (HGNC:11998)
Evidence Code: BS2 — Supporting
Modification Type: Disease-specific
Observed in 2-7 cancer free 60+ year old females.
Gene: TP53 (HGNC:11998)
Evidence Code: BS3 — Strong
Modification Type: Disease-specific,Strength
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.
Gene: TP53 (HGNC:11998)
Evidence Code: BS3 — Supporting
Modification Type: Disease-specific,Strength
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
Gene: TP53 (HGNC:11998)
Evidence Code: BS4 — Strong
Modification Type: Disease-specific
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.
Gene: TP53 (HGNC:11998)
Evidence Code: BP2 — Supporting
Modification Type: Disease-specific
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
Gene: TP53 (HGNC:11998)
Evidence Code: BP4 — Supporting
Modification Type: Disease-specific,Strength
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
Gene: TP53 (HGNC:11998)
Evidence Code: BP7 — Supporting
Modification Type: Disease-specific
Concordance of MaxEntScan and HSF; If a new alternate site is predicted, compare strength to native site in interpretation.