TP53 c.833C>T, p.(Pro278Leu)

Reasoning

The ClinGen TP53 VCEP Functional-worksheet.xlsx Supplementary Table S3 contains the exact protein-change row P278L, corresponding to NM_000546.6:c.833C>T / p.Pro278Leu. The row records Kato class Non-functional, Funk class LOF, Giacomelli class LOF, Kotler class LOF, Kawaguchi class NA, and a pre-assigned PS3 code. This satisfies the VCEP's strong PS3 rule because the variant is non-functional on Kato data and loss of function by the majority of other eligible assays: three of the three additional available assays listed in the row are LOF. The VCEP flowchart identifies Kato, Funk, Giacomelli, Kotler, and Kawaguchi as eligible functional studies.

VCEP rule

Non-functional on Kato et al. data **AND** loss of function (LOF) by the majority of other eligible assays

Evidence considered

• Functional-worksheet.xlsx, Supplementary Table S3, row P278L: Kato class = Non-functional; Funk class = LOF; Giacomelli class = LOF; Kotler class = LOF; Kawaguchi class = NA; preliminary functional code = PS3.
• Flowchart-for-application-of-functional-rule-codes.pdf, page 1: eligible functional studies include Kato (PMID: 12826609), Funk (PMID 39774325), Giacomelli (PMID: 30224644), Kotler (PMID: 29979965), and Kawaguchi (PMID: 16007150).
• The exact nucleotide and three-letter protein notations were not present in the functional worksheet text, but the exact one-letter protein change P278L was present and matches the case normalization p.(Pro278Leu)/p.(P278L).

Still missing

• The functional flowchart contains no variant-specific row for c.833C>T, p.Pro278Leu, or p.P278L; it supplies assay eligibility guidance rather than per-variant results.

Sources

Reasoning

PM2 is met at supporting strength. The TP53 VCEP requires an allele frequency below 0.00003 in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group's frequency must be below 0.00004, with founder-effect groups ignored. gnomAD v4.1 all-comers reports 1/1,614,026 alleles (AF 6.195687058324959e-07), zero homozygotes, and no eligible ancestry group with multiple variant alleles; the highest observed frequency is in the excluded Remaining group and is still below 0.00004. The VCEP does not require a non-cancer or exome-only source, so the available all-comers gnomAD v4.1 data are used; failed non-cancer queries are not treated as absence or rarity evidence.

VCEP rule

This rule should be applied at supporting level. Variant should have an allele frequency of less than 0.00003 (0.003%) in gnomAD or another large sequenced population. If multiple alleles are present within any genetic ancestry group, allele frequency in that group must be <0.00004 (0.004%). Genetic ancestry groups influenced by founder effects (such as Ashkenazi Jewish, Finnish, Amish, Middle Eastern, and “Remaining”) should be ignored. If the variant being assessed does not meet any population rule codes (PM2, BA1, BS1) **AND** has a total allele frequency >0.00003 with no single genetic ancestry group having multiple alleles with a frequency >0.00004, curators should recalculate the total allele frequency based on the number of alleles with variant allele fraction (VAF) >0.35 to assess whether PM2 may be met after excluding the low VAF alleles which are likely to represent clonal hematopoiesis of indeterminant potential (CHIP) contamination in the database. This can be done by visualizing the “allele balance” for heterozygotes under the genotype quality metrics for a given variant. By hovering over the histogram bars, the number of variant carriers for each bar between 0.35 and 0.65 can be totaled and this can be used to revise the allele count to determine the allele frequency that can be used to assess if PM2_Supporting can be met. In general, the most recent version of gnomAD should be used when available; however, other population databases or earlier versions of gnomAD may be utilized if they are able to provide information the curator deems necessary for optimal variant classification (e.g, they would provide superior information for a particular variant type; have a larger sample size; or better representation for certain subpopulations, etc.)

Evidence considered

• ClinGen TP53 VCEP v2.4 PM2 rule: apply at supporting level when AF is <0.00003; if multiple alleles occur within an ancestry group, that group's AF must be <0.00004; founder-effect groups including Remaining are ignored.
• gnomAD v4.1 all-comers total: 1/1,614,026 alleles, AF 6.195687058324959e-07, homozygotes 0.
• gnomAD v4.1 highest reported subpopulation: Remaining individuals, 1/62,508 alleles, AF 1.599795226211045e-05, homozygotes 0; Remaining is ignored under the VCEP rule and the frequency is nevertheless below 0.00004.
• The VCEP text does not specify a non-cancer or exome-only population source for PM2; therefore the available all-comers gnomAD v4.1 entry is the default source. The non-cancer query results are failed/unknown and were not used as evidence.

Sources

Reasoning

The variant is a missense substitution, and the TP53 VCEP Supplementary Table S2 pre-assigns PP3_moderate for c.833C>T / p.Pro278Leu: BayesDel class C65 with score 0.583698. This governing lookup-table assignment is applied directly. The accompanying SpliceAI result has a maximum delta score of 0.006, below the VCEP's 0.2 splice-impact threshold, but it is not used to create a second PP3/BP4/BP7 code or to override the pre-assigned PP3_moderate assignment.

VCEP rule

**Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants)_ aGVGD Class C65 and BayesDel score ≥ 0.16

Evidence considered

• PP3-BP4-codes.xlsx, Supplementary Table S2 row: c.833C>T | p.Pro278Leu | Class C65 | BayesDel 0.583698 | PP3_moderate | 0.01.
• The VCEP flowchart states that PP3/BP4/BP7 application uses no predicted splicing difference with SpliceAI < 0.2; the case SpliceAI maximum delta score is 0.006.
• The exact variant notations c.833C>T, p.Pro278Leu, and p.P278L were searched in all three on-record TP53 files named for this group; the exact lookup row was found in PP3-BP4-codes.xlsx only.

Still missing

• No exact c.833C>T, p.Pro278Leu, or p.P278L entry was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf.txt; the flowchart is rule guidance rather than a variant lookup table.
• No exact c.833C>T, p.Pro278Leu, or p.P278L entry was found in TP53-single-amino-acid-deletions-BayesDel-scores-(1).xlsx.txt; that file covers single amino acid in-frame deletions, not this missense variant.

Sources

Reasoning

BA1 is not met. The TP53 VCEP requires a filtering allele frequency (FAF) of at least 0.001 in an eligible gnomAD continental subpopulation of a single genetic ancestry group, with at least 2,000 alleles tested and at least 2 variant alleles present, excluding founder-effect groups including Remaining. gnomAD v4.1 reports one total allele among 1,614,026 alleles (AF 6.195687058324959e-07), and the highest subpopulation frequency is in the explicitly excluded Remaining individuals group (1/62,508; AF 1.599795226211045e-05); all eligible continental subpopulations have zero observed alleles. Therefore the BA1 threshold is not reached.

VCEP rule

Filtering allele frequency (FAF) of ≥ 0.001 or 0.1% in gnomAD continental subpopulations of a single genetic ancestry group (excluding genetic ancestry groups influenced by founder effects, such as Ashkenazi Jewish, Finnish, Amish, Middle Eastern, and “Remaining”). Genetic ancestry group must have ≥2,000 alleles tested and a minimum of 2 alleles present. Caution should be exerted if the majority of alleles have a variant allele fraction ("allele balance" in gnomAD) below 0.35. To set the stand-alone benign FAF cutoff, we used the FAF cutoff established for BS1 (0.0003) and increased this cutoff by one order of magnitude to come to a value of 0.001. In general, the most recent version of gnomAD should be used when available; however, other population databases or earlier versions of gnomAD may be utilized if they are able to provide information the curator deems necessary for optimal variant classification (e.g, they would provide superior information for a particular variant type; have a larger sample size; or better representation for certain subpopulations, etc.)

Evidence considered

• ClinGen TP53 VCEP v2.4 BA1 rule: FAF must be ≥0.001 in an eligible continental ancestry subpopulation, with ≥2,000 alleles tested and ≥2 alleles present; founder-effect groups including Remaining are excluded.
• gnomAD v4.1, all-comers total: 1/1,614,026 alleles, total AF 6.195687058324959e-07, homozygotes 0.
• gnomAD v4.1, highest reported subpopulation: Remaining individuals, 1/62,508 alleles, AF 1.599795226211045e-05, homozygotes 0; this population is excluded by the VCEP rule.
• Eligible gnomAD v4.1 continental ancestry groups each have zero observed variant alleles for this variant.

Sources

Reasoning

BS1 is not met. The TP53 VCEP requires FAF of at least 0.0003 but less than 0.001 in an eligible continental subpopulation, with at least 2,000 alleles tested and at least 2 variant alleles present, excluding founder-effect groups including Remaining. gnomAD v4.1 has one total allele overall and one allele in the highest-frequency Remaining individuals group (1/62,508; AF 1.599795226211045e-05), which is excluded; every eligible continental subpopulation has zero observed alleles. No eligible subpopulation reaches the BS1 lower threshold or the required allele count.

VCEP rule

Filtering allele frequency (FAF) of ≥ 0.0003 but < 0.001 in gnomAD continental subpopulations of a single genetic ancestry group (excluding genetic ancestry groups influenced by founder effects, such as Ashkenazi Jewish, Finnish, Amish, Middle Eastern, and “Remaining”). Genetic ancestry group must have ≥2,000 alleles tested and a minimum of 2 alleles present. Caution should be exerted if the majority of alleles have a variant allele fraction ( “allele balance” in gnomAD) below 0.35. To set the strong benign FAF cutoff, we used a Whiffin-Ware calculation using prevalence of 1 in 5,000 (Lalloo, et al., 2006 PMID: 16644204). Genetic and allelic heterogeneity were set at 100% and penetrance at 30%. In general, the most recent version of gnomAD should be used when available; however, other population databases or earlier versions of gnomAD may be utilized if they are able to provide information the curator deems necessary for optimal variant classification (e.g, they would provide superior information for a particular variant type; have a larger sample size; or better representation for certain subpopulations, etc.)

Evidence considered

• ClinGen TP53 VCEP v2.4 BS1 rule: FAF must be ≥0.0003 but <0.001 in an eligible continental ancestry subpopulation, with ≥2,000 alleles tested and ≥2 alleles present; founder-effect groups including Remaining are excluded.
• gnomAD v4.1, all-comers total: 1/1,614,026 alleles, total AF 6.195687058324959e-07, homozygotes 0.
• gnomAD v4.1, highest reported subpopulation: Remaining individuals, 1/62,508 alleles, AF 1.599795226211045e-05; this population is excluded by the VCEP rule.
• Eligible gnomAD v4.1 continental ancestry groups each have zero observed variant alleles for this variant.

Sources

Reasoning

BS3 is not met because the governing Functional-worksheet.xlsx row for P278L records Non-functional Kato activity and LOF in the Funk, Giacomelli, and Kotler assay columns. These findings are incompatible with either VCEP BS3 path: the strong path requires functional Kato data and no LOF by the majority of eligible assays, while the supporting path requires partially functional Kato data and no LOF by all available assays. The VCEP pre-assigned code for the row is PS3, not BS3.

VCEP rule

Functional on Kato et al. data **AND** no loss of function (LOF) by the majority of available eligible assays ... Partially functional on Kato et al. data **AND** no evidence of loss of function (LOF) by **all** available assays

Evidence considered

• Functional-worksheet.xlsx, Supplementary Table S3, row P278L: Kato class = Non-functional; Funk class = LOF; Giacomelli class = LOF; Kotler class = LOF; Kawaguchi class = NA; preliminary functional code = PS3, with no BS3 assignment.
• The VCEP strong BS3 path requires functional Kato data and no LOF by the majority of available eligible assays; the supporting path requires partially functional Kato data and no LOF by all available assays. The P278L row meets neither condition.

Still missing

• The functional flowchart contains no variant-specific row for c.833C>T, p.Pro278Leu, or p.P278L; it supplies assay eligibility guidance rather than per-variant results.

Sources

Reasoning

The variant is a missense substitution and has BayesDel class C65 with score 0.583698. Although SpliceAI predicts no splice impact with a maximum delta score of 0.006 (<0.2), the TP53 VCEP BP4 rule explicitly excludes C65 missense variants from BP4 application; therefore BP4 is not met.

VCEP rule

**Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants):_ BayesDel ≤ -0.008 irrespective of aGVGD score (except C65, in this case do not apply BP4_Moderate) AND no predicted differences in splicing (SpliceAI < 0.2) ... **Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants):_ BayesDel < 0.16 and > -0.008 irrespective of aGVGD score (except C65, this case do not apply BP4) AND no predicted differences in splicing (SpliceAI < 0.2)

Evidence considered

• PP3-BP4-codes.xlsx, Supplementary Table S2 row: c.833C>T | p.Pro278Leu | Class C65 | BayesDel 0.583698 | PP3_moderate | 0.01; no BP4 code is assigned.
• The VCEP BP4 missense rule states that BayesDel <0.16 and >-0.008 is required, with the exception that C65 variants do not receive BP4, and also requires SpliceAI <0.2; the observed maximum delta is 0.006.
• The exact variant notations c.833C>T, p.Pro278Leu, and p.P278L were searched in all three on-record TP53 files named for this group; no exact BP4 assignment was found.

Still missing

• No exact c.833C>T, p.Pro278Leu, or p.P278L entry was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf.txt; the flowchart is rule guidance rather than a variant lookup table.
• No exact c.833C>T, p.Pro278Leu, or p.P278L entry was found in TP53-single-amino-acid-deletions-BayesDel-scores-(1).xlsx.txt; that file covers single amino acid in-frame deletions, not this missense variant.

Sources

Reasoning

The variant is p.Pro278Leu and has a published exact-variant observation, but the available evidence does not identify a previously established pathogenic variant with the same amino-acid change arising from a different nucleotide change. The VCEP requires PS1 comparison with variants asserted as pathogenic or likely pathogenic under the TP53 VCEP specifications and requires no splicing difference; SpliceAI is 0.006, below 0.2, but the required alternate-nucleotide comparator and VCEP-qualified prior assertion are not available.

VCEP rule

This rule code can only be used to compare variants asserted as pathogenic or likely pathogenic following the ClinGen _TP53_ VCEP’s specifications. Must confirm there is no difference using RNA data or SpliceAI (SpliceAI < 0.2). ... Can be applied to variants asserted as Pathogenic following the _TP53_ VCEP’s specifications.

Evidence considered

• NM_000546.6:c.833C>T encodes NP_000537.3:p.(Pro278Leu).
• Table 4, row 12 of Gonzalez et al. (PMID:19556618) reports the exact p.Pro278Leu variant in a clinical family history, but it is the same nucleotide-defined variant and does not establish a differently encoded comparator under the TP53 VCEP.
• SpliceAI maximum delta score is 0.006, satisfying the VCEP's no-splicing-difference requirement if a qualifying comparator were available.

Still missing

• A previously established pathogenic or likely pathogenic TP53 variant encoding p.Pro278Leu through a different nucleotide change is needed.
• The prior comparator must be classified under the TP53 VCEP specifications.

Sources

Reasoning

PMID:19556618 reports p.Pro278Leu in a family-history summary as a non-confirmed de novo mutation: the father and brother reportedly did not carry the variant, but the mother was not tested. The report lists liposarcoma, two breast cancers, two histiocytomas, and adenocarcinoma, yet does not provide the proband's cancer age/details needed to assign points from the VCEP LFS-cancer table, nor does it establish confirmed maternity and paternity. The governing VCEP table was searched for c.833C>T, p.Pro278Leu, and p.P278L, with no variant-specific pre-assigned PS2 code found. Therefore the VCEP point threshold cannot be evaluated reliably.

VCEP rule

1 point...2-3...4-7...≥ 8

Evidence considered

• PMID:19556618, Table 4, non-confirmed de novo TP53 mutations, row 12: p.Pro278Leu is associated with liposarcoma, two breast cancers, two histiocytomas, and adenocarcinoma; the family history lists a daughter, five brothers, two sisters, father, MFS, and two sons with multiple tumours, with linkage analysis.
• PMID:19556618, Table 4 footnote: Speiser et al. reported a constitutional de novo mutation in exon 8; the case summary states the mother was not tested, while the father and brother did not carry the variant.
• Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf, PS2 Code Strength Based on Total Points: PS2_Supporting = 1, PS2_Moderate = 2-3, PS2 = 4-7, PS2_Very Strong = >=8; no row for c.833C>T, p.Pro278Leu, or p.P278L was found.

Still missing

• Parental testing is incomplete: the mother was not tested, so confirmed maternity and paternity are unavailable.
• The report does not identify the proband's cancer diagnoses and ages sufficiently to assign VCEP LFS-cancer points.
• No variant-specific pre-assigned PS2 code was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf after searching c.833C>T, p.Pro278Leu, and p.P278L.

Sources

Reasoning

The queried variant is reported in Table 4 of Gonzalez et al. as p.Pro278Leu, with liposarcoma, two breast cancers, two histiocytomas, and adenocarcinoma in the described family. However, the available report does not provide the proband's ages or establish Revised Chompret or Classic LFS criteria, so the VCEP PS4 point total cannot be determined. The governing PS4 thresholds are 1-1.5 points for Supporting, 2-3.5 points for Moderate, ≥ 4-7.5 points for Strong, and ≥ 8 points for Very Strong.

VCEP rule

1-1.5 points ... 2-3.5 points ... ≥ 4-7.5 points ... ≥ 8 points

Evidence considered

• Gonzalez et al. 2009, PMID:19556618, Table 4, row 12: c.833C>T/p.Pro278Leu is listed as a missense mutation associated with liposarcoma, breast, breast, histiocytoma, histiocytoma, and adenocarcinoma; the report describes it as a non-confirmed de novo mutation.
• ClinGen TP53 VCEP PS4-Points-Table.pdf: PS4_Supporting = 1-1.5 points, PS4_Moderate = 2-3.5 points, PS4 = 4-7.5 points, and PS4_Very Strong = ≥ 8 points.

Still missing

• The PS4-Points-Table.pdf was searched for c.833C>T, p.Pro278Leu, and p.P278L; no variant-specific entry was found because the file is a generic scoring table.
• The available variant report does not provide the proband's ages or enough clinical detail to determine Revised Chompret, Classic LFS, or HER2-positive breast-cancer point eligibility.

Sources

Reasoning

Residue 278 is outside the six codons explicitly listed by the TP53 VCEP for PM1 (175, 245, 248, 249, 273, and 282). The VCEP also permits PM1 at moderate strength for a germline missense variant seen in cancerhotspots.org v2 with at least 10 somatic occurrences for the same amino-acid change, but the available hotspot result supplies no occurrence count and the COSMIC count of 155 is not a cancerhotspots.org v2 count. vcep_materials.json has no domain_tables entry for TP53, so no authoritative domain-table path is available.

VCEP rule

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. ... Missense variants within the following codons using transcript NM\_00546.4: 175, 245, 248, 249, 273, 282. This code weight can also be used for germline missense variants seen in cancerhotspots.org with ≥ 10 somatic occurrences for the same amino acid change.

Evidence considered

• The VCEP's explicitly listed PM1 codons are 175, 245, 248, 249, 273, and 282; residue 278 is not among them.
• The hotspot result reports that TP53 P278 lies in a statistically significant hotspot but provides no same-amino-acid somatic occurrence count.
• COSMIC reports COSV52678063 for the exact variant with n = 155 somatic observations; this is not the cancerhotspots.org v2 count specified by the VCEP.
• vcep_materials.json domain_tables is empty for TP53.

Still missing

• A cancerhotspots.org v2 record documenting at least 10 somatic occurrences for the same p.Pro278Leu amino-acid change is needed, or an authoritative TP53 domain table entry.
• The COSMIC count cannot substitute for the VCEP's cancerhotspots.org v2 requirement.

Sources

Reasoning

Two alternate missense substitutions at residue 278, p.Pro278Ser and p.Pro278Thr, are reported in a Li-Fraumeni family study, but the paper does not establish either comparator as pathogenic or likely pathogenic according to the TP53 VCEP specifications. The available PM5 candidate collection found no usable same-residue VCEP-qualified comparators, and no Grantham comparison for a qualifying comparator can therefore be completed.

VCEP rule

This code can be applied for a missense change at an amino acid residue where one or more pathogenic/likely pathogenic variants have been identified. The other variant must be interpreted as pathogenic or likely pathogenic following the ClinGen _TP53_ VCEP’s specifications. The previously established pathogenic/likely pathogenic variant must reach a classification of pathogenicity without PM5. ... Grantham should be used to compare the variants. The variant being evaluated must be equal or worse (value is greater than) than the known pathogenic variant (i.e. the variant residue should be equally chemically different or more chemically different than the wild type residue in comparison to the wild type residue). Splicing should be ruled out with either RNA data or SpliceAI (SpliceAI < 0.2). ... Missense variant at an amino acid residue where 1 different missense variant previously determined to be pathogenic according to the _TP53_ VCEP’s specifications has been seen before.

Evidence considered

• Güran et al. (PMID:15993273) reports germline p.Pro278Ser and p.Pro278Thr in two Li-Fraumeni families, but does not provide VCEP classifications or the clinical-data requirements needed to qualify them for PM5.
• The PM5 candidate collection contains zero same-residue candidates and zero expert-panel or non-expert majority pathogenic/likely pathogenic candidates.
• No qualifying comparator is available for the VCEP-required Grantham comparison or the no-PM5 classification check.

Still missing

• A different missense variant at Pro278 classified as pathogenic or likely pathogenic under TP53 VCEP specifications is needed.
• The comparator must reach its pathogenic classification without PM5, and Grantham comparison must be documented.

Sources

Reasoning

PMID:19556618 reports two sons with multiple tumours and multiple unaffected relatives in the family history, but it does not report variant testing or phenotype/variant status for those relatives in a way that establishes cosegregation. No meiosis count can therefore be derived. The VCEP table was searched for c.833C>T, p.Pro278Leu, and p.P278L, with no variant-specific pre-assigned PP1 code found.

VCEP rule

Cosegregation must be observed in ≥ 7 meioses across > 1 family...Cosegregation must be observed in 5-6 meioses in/across 1 or more families...Cosegregation must be observed in 3-4 meioses in/across 1 or more families

Evidence considered

• PMID:19556618, Table 4, row 12: the family history lists a daughter with no cancer, five brothers with no cancer, two sisters with no cancer, a father with no cancer, MFS with no cancer, and two sons with multiple tumours; linkage is reported, but relative-specific variant segregation results are not given.
• TP53 VCEP CSPEC v2.4, PP1 thresholds: Supporting requires 3-4 cosegregating meioses, Moderate requires 5-6, and Strong requires at least 7 across more than 1 family; no countable meioses are available.
• Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.833C>T, p.Pro278Leu, and p.P278L; no variant-specific pre-assigned PP1 code was found.

Still missing

• Variant testing results for the affected sons and other informative relatives are not provided.
• The number of informative meioses cannot be determined from the available report.
• No variant-specific pre-assigned PP1 code was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf after searching c.833C>T, p.Pro278Leu, and p.P278L.

Sources

Reasoning

The TP53 VCEP defines PP4 from low-VAF observations on multigene panel testing: at least two independent observations with VAF 5-25% for Moderate, or observation with VAF 5-35% for Supporting. The available evidence does not report qualifying VAF observations for c.833C>T/p.Pro278Leu, and no PP4 strength can therefore be assigned.

VCEP rule

At least 2 independent observations of the variant with VAF 5-25%. ... Observation of the variant with VAF 5-35% (i.e., once or multiple times with VAF >25-35% and/or once with VAF 5-25%)

Evidence considered

• TP53 VCEP PP4 rule: Moderate requires at least 2 independent observations with VAF 5-25%; Supporting requires observation with VAF 5-35% (including once or multiple times with VAF >25-35% and/or once with VAF 5-25%).
• The reviewed variant-specific clinical report describes germline family observations but provides no qualifying multigene-panel VAF data.

Still missing

• No multigene-panel VAF values or independent low-VAF observations are available for c.833C>T/p.Pro278Leu.

Sources

Reasoning

BS2 cannot be assessed from the available evidence. The TP53 VCEP requires counts of unrelated females aged at least 60 years without cancer from a single source, with separate thresholds for supporting (2-3), moderate (4-7), and strong (≥8) evidence. gnomAD reports zero homozygotes, but it does not provide the required variant-carrier sex, age, cancer-status, unrelatedness, and single-source cohort information; zero homozygotes therefore cannot establish any BS2 strength.

VCEP rule

≥ 8 unrelated females who have reached at least 60 years of age without cancer. These individuals all must have come from a single source (single lab, database, etc). Cases cannot be counted across sources. Individuals with a diagnosis of sarcoma ≥ 61 years of age should not be counted towards the BS2 total. ... 4-7 unrelated females who have reached at least 60 years of age without cancer. These individuals all must have come from a single source (single lab, database, etc). Cases cannot be counted across sources. Individuals with a diagnosis of sarcoma ≥ 61 years of age should not be counted towards the BS2 total. ... 2-3 unrelated females who have reached at least 60 years of age without cancer. These individuals all must have come from a single source (single lab, database, etc). Cases cannot be counted across sources. Individuals with a diagnosis of sarcoma ≥ 61 years of age should not be counted towards the BS2 total.

Evidence considered

• ClinGen TP53 VCEP v2.4 BS2 rule requires unrelated females aged ≥60 years without cancer from one source; 2-3 support, 4-7 moderate, and ≥8 strong.
• gnomAD v4.1 reports homozygotes = 0, but provides no qualifying age-, sex-, cancer-status-, unrelatedness-, or single-source carrier count for BS2.

Still missing

• A single-source cohort with variant-carrier sex, age, cancer status, unrelatedness, and sarcoma history is required to assess BS2.

Sources

Reasoning

The TP53 VCEP defines BS4 as lack of segregation in affected family members with LFS-associated cancers. PMID:19556618 reports affected relatives with multiple tumours, but it does not state whether those affected relatives were tested for p.Pro278Leu or whether they lacked the variant. The available evidence therefore does not establish lack of segregation.

VCEP rule

Lack of segregation in affected family members (i.e. family members diagnosed with LFS-associated cancers as described in Table of LFS Cancers and Points for PS2 and PP1 Code Application).

Evidence considered

• PMID:19556618, Table 4, row 12: two sons with multiple tumours are listed, but the table does not provide their p.Pro278Leu testing results.
• TP53 VCEP CSPEC v2.4, BS4 rule: affected-family-member non-segregation requires lack of segregation in family members diagnosed with LFS-associated cancers.

Still missing

• Variant testing results for the affected sons and any other affected family members are not provided.
• No variant-specific pre-assigned BS4 code was identified in the governing VCEP materials.

Sources