TP53 c.665C>T, p.Pro222Leu

Reasoning

The TP53 VCEP specifies PM2 at supporting strength when total allele frequency is below 0.00003 and, when multiple alleles occur in an ancestry group, that group's frequency is below 0.00004; founder-effect groups are ignored. Using the default all-comers gnomAD v4.1 dataset, total AF is 1.17722e-05 (19/1613970; homozygotes = 0). The largest eligible ancestry-group AF with multiple alleles is South Asian at 2.19568e-05 (2/91088), below 0.00004; European non-Finnish has 17 alleles at AF 1.44070e-05. PM2_Supporting is met.

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.

Evidence considered

• ClinGen TP53 VCEP PM2 rule: apply at supporting level when allele frequency is <0.00003; if multiple alleles occur in an ancestry group, that group's frequency must be <0.00004; founder-effect groups including Remaining are ignored.
• gnomAD v4.1 all-comers: total AF 1.1772213857754481e-05 (19/1613970 alleles), total homozygotes = 0.
• gnomAD v4.1 South Asian: 2/91088 alleles, AF 2.1956789039170913e-05, homozygotes = 0; European non-Finnish: 17/1179980 alleles, AF 1.4407023847861829e-05, homozygotes = 0.
• The VCEP rule does not require a non-cancer or exome-only source, so the default all-comers gnomAD v4.1 totals were used.

Sources

Reasoning

The governing ClinGen TP53 VCEP Functional-worksheet.xlsx Supplementary Table S3 row for P222L reports Kato class Functional and noLOF for Funk, Giacomelli, and Kotler, with Kawaguchi NA, and assigns the preliminary functional code BS3. This matches the VCEP BS3 Strong rule requiring functional Kato data and no LOF by the majority of available eligible assays: all three available follow-up assays are noLOF, while Kawaguchi is not available. The VCEP flowchart independently maps a missense variant with Functional Kato data and noLOF by the majority of available assays to BS3.

VCEP rule

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

Evidence considered

• ClinGen TP53 VCEP Functional-worksheet.xlsx, Supplementary Table S3, row P222L: Kato class Functional; Funk noLOF; Giacomelli noLOF; Kotler noLOF; Kawaguchi NA; preliminary functional code BS3.
• ClinGen TP53 VCEP functional flowchart: Missense variants with Kato data available and Functional Kato results plus noLOF by the majority of available assays receive BS3.
• Grochova et al. (PMID:17724467) directly studied P222L in yeast and reported activity nearly reaching wild-type at 35 °C; the study's assay context is concordant with the VCEP worksheet's no-LOF classification.

Sources

Reasoning

The variant is a TP53 missense change, and the governing ClinGen TP53 VCEP Functional-worksheet.xlsx Supplementary Table S3 row for P222L reports Kato class Functional, Funk noLOF, Giacomelli noLOF, Kotler noLOF, and Kawaguchi NA, with the pre-assigned functional code BS3. This does not satisfy any PS3 path: PS3 Strong requires non-functional Kato data plus LOF by the majority of other eligible assays; PS3 Moderate requires partially functional Kato data plus majority LOF; and PS3 Supporting requires non-functional Kato data plus abnormal Kawaguchi data. The exact-variant functional assay row therefore supports benign functional evidence rather than loss of function.

VCEP rule

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

Evidence considered

• ClinGen TP53 VCEP Functional-worksheet.xlsx, Supplementary Table S3, row P222L: Kato class Functional; Funk noLOF; Giacomelli noLOF; Kotler noLOF; Kawaguchi NA; preliminary functional code BS3.
• ClinGen TP53 VCEP functional flowchart: for missense variants with Kato data, PS3 requires non-functional or partially functional Kato results together with LOF in the specified eligible-assay pattern; the P222L row instead reports Functional Kato data and noLOF in the available follow-up assays.
• Grochova et al. (PMID:17724467) directly studied P222L in yeast and reported activity nearly reaching wild-type at 35 °C, providing variant-specific functional context consistent with the VCEP worksheet's non-LOF classification.

Sources

Reasoning

The TP53 VCEP specifies PM1 for missense variants at codons 175, 245, 248, 249, 273, or 282, or for germline missense variants seen in cancerhotspots.org with at least 10 somatic occurrences for the same amino-acid change; the supporting route requires 2–9 cancerhotspots.org somatic occurrences. The variant is p.Pro222Leu, outside all six specified codons, and the cancerhotspots.org result reports no hotspot row. COSMIC reports five occurrences, but COSMIC is not the VCEP-named hotspot source and therefore cannot satisfy the PM1 hotspot route. vcep_materials.json contains no TP53 domain-table entry, so no additional authoritative domain route applies.

VCEP rule

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. ... Missense variants seen in cancerhotspots.org with 2-9 somatic occurrences for the same amino acid change.

Evidence considered

• TP53 VCEP PM1 moderate rule: eligible codons are 175, 245, 248, 249, 273, and 282; the alternative requires at least 10 cancerhotspots.org somatic occurrences for the same amino-acid change.
• TP53 VCEP PM1 supporting rule: cancerhotspots.org must show 2–9 somatic occurrences for the same amino-acid change.
• The assessed variant is p.Pro222Leu (residue 222), not one of the six specified codons.
• Cancer Hotspots result for TP53 P222: no result and no hotspot row found.
• COSMIC reports COSV52909202 with n = 5 somatic occurrences, but the TP53 VCEP names cancerhotspots.org, not COSMIC, for the hotspot route.
• vcep_materials.json domain_tables is empty for TP53; therefore no authoritative TP53 domain-table entry adds a PM1 route.

Sources

Reasoning

The variant is a missense substitution, NM_000546.6:c.665C>T (p.Pro222Leu/P222L). The governing TP53 PP3-BP4 spreadsheet contains the exact row c.665C>T, p.Pro222Leu: BayesDel class C0, BayesDel score 0.224549, assigned code "No evidence," and splice value 0.05. The VCEP missense PP3 paths require either aGVGD C65 with BayesDel >= 0.16 for moderate strength or aGVGD C25-C55 with BayesDel >= 0.16 for supporting strength; the row is C0 and is explicitly pre-assigned "No evidence." SpliceAI is available with maximum delta score 0.045, below the VCEP splice-effect threshold of 0.2, so the splice path is not met either. The flowchart and the single-amino-acid-deletions BayesDel spreadsheet were searched for c.665C>T, p.Pro222Leu, and p.P222L and had no matching entry; the deletion spreadsheet is outside this missense variant's scope.

VCEP rule

**Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants)_ aGVGD Class C65 and BayesDel score ≥ 0.16 ... **Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants)_ aGVGD class C25-C55 and BayesDel score ≥ 0.16 **Exonic (including silent variants and apparent “missense” variants or “single amino acid inframe deletions” for which there is a predicted splice effect) or Intronic Splice Variants (excluding ± 1,2 positions):** SpliceAI ≥ 0.2

Evidence considered

• PP3-BP4-codes.xlsx, Supplementary Table S2 row: c.665C>T | p.Pro222Leu | Class C0 | BayesDel 0.224549 | No evidence | 0.05.
• The exact variant was searched as c.665C>T, p.Pro222Leu, and p.P222L in the governing PP3/BP4 lookup, flowchart text, and single-amino-acid-deletions BayesDel text.
• SpliceAI Lookup for NM_000546.6:c.665C>T: DS_AG 0.0, DS_AL 0.012, DS_DG 0.0, DS_DL 0.045; maximum delta score 0.045.

Still missing

• No c.665C>T, p.Pro222Leu, or p.P222L entry was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf.txt; the flowchart is a rule document rather than a variant lookup table.
• No c.665C>T, p.Pro222Leu, or p.P222L 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 TP53 VCEP requires a filtering allele frequency (FAF) of at least 0.001 in one eligible continental ancestry group, with at least 2,000 alleles tested and at least 2 variant alleles. In gnomAD v4.1, the highest eligible ancestry-group frequency is South Asian AF 2.19568e-05 (2/91088; grpmax FAF 8.78e-06), far below 0.001. Founder-effect and Remaining groups are excluded by the VCEP rule. Therefore BA1 is not met.

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.

Evidence considered

• ClinGen TP53 VCEP BA1 rule: eligible ancestry-group FAF must be ≥0.001, with ≥2,000 alleles tested and at least 2 variant alleles; founder-effect groups and Remaining are excluded.
• gnomAD v4.1: South Asian was the highest eligible ancestry group at AF 2.19568e-05 (2/91088 alleles), with grpmax FAF 8.78e-06; homozygotes = 0.
• gnomAD v4.1 source_data: total AF 1.1772213857754481e-05 (19/1613970 alleles); no eligible ancestry group approached FAF 0.001.

Sources

Reasoning

The TP53 VCEP requires eligible ancestry-group FAF of at least 0.0003 but less than 0.001, with at least 2,000 alleles tested and at least 2 variant alleles. The highest eligible gnomAD v4.1 ancestry-group frequency is South Asian AF 2.19568e-05 with grpmax FAF 8.78e-06, below 0.0003. The excluded Remaining group is not used. Therefore BS1 is not met.

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.

Evidence considered

• ClinGen TP53 VCEP BS1 rule: eligible ancestry-group FAF must be ≥0.0003 and <0.001, with ≥2,000 alleles tested and at least 2 variant alleles; founder-effect groups and Remaining are excluded.
• gnomAD v4.1: South Asian was the highest eligible ancestry group at AF 2.19568e-05 (2/91088 alleles), while grpmax FAF was 8.78e-06; homozygotes = 0.
• gnomAD v4.1 source_data: total AF 1.1772213857754481e-05 (19/1613970 alleles).

Sources

Reasoning

The variant is a missense substitution, NM_000546.6:c.665C>T (p.Pro222Leu/P222L). The governing TP53 PP3-BP4 spreadsheet contains the exact row c.665C>T, p.Pro222Leu with BayesDel class C0, BayesDel score 0.224549, assigned code "No evidence," and splice value 0.05. The VCEP missense BP4 supporting path requires BayesDel < 0.16 and > -0.008, except that C65 cannot receive BP4, together with SpliceAI < 0.2; the observed BayesDel score is 0.224549 and therefore fails the required BayesDel interval. BP4 moderate also requires BayesDel <= -0.008 and is not met. The exact lookup row's pre-assigned "No evidence" governs. The flowchart and the single-amino-acid-deletions BayesDel spreadsheet were searched for c.665C>T, p.Pro222Leu, and p.P222L and had no matching entry; the deletion spreadsheet is outside this missense variant's scope.

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.665C>T | p.Pro222Leu | Class C0 | BayesDel 0.224549 | No evidence | 0.05.
• SpliceAI Lookup for NM_000546.6:c.665C>T: maximum delta score 0.045, below the VCEP no-predicted-splice-impact cutoff of 0.2.

Still missing

• No c.665C>T, p.Pro222Leu, or p.P222L entry was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf.txt; the flowchart is a rule document rather than a variant lookup table.
• No c.665C>T, p.Pro222Leu, or p.P222L 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 TP53 VCEP restricts PS1 to a same-amino-acid change previously established as pathogenic or likely pathogenic under the TP53 VCEP specifications, with no RNA or SpliceAI difference. The available exact P222L reports do not establish a prior pathogenic or likely pathogenic comparator: PMID:17724467 reports P222L with temperature-dependent assay findings, and PMID:19336573 lists P222L as a neutral missense mutation. No qualifying prior pathogenic P222L assertion is available in the supplied evidence, so PS1 cannot be adjudicated.

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).

Evidence considered

• TP53 VCEP PS1 rule: same-amino-acid comparison is limited to variants asserted as Pathogenic or Likely Pathogenic following the TP53 VCEP specifications, and splicing must be excluded with RNA data or SpliceAI < 0.2.
• PMID:17724467, Results and Table 1: exact P222L was studied in yeast; activity nearly reached wild-type at 35 °C and the paper does not establish the variant as pathogenic or likely pathogenic under the TP53 VCEP.
• PMID:19336573, Table 1, tumor sample B150: exact P222L was reported at 50% abundance and listed among neutral missense mutations; this does not establish a qualifying pathogenic comparator.

Still missing

• A prior TP53 variant with the same p.Pro222Leu amino-acid change, independently established as pathogenic or likely pathogenic under the TP53 VCEP specifications, is not documented.

Sources

Reasoning

The TP53 VCEP assigns PS2 by the LFS-cancer point total for de novo observations, but the reviewed case evidence contains no documented proband de novo event, parental testing, parental phenotype, or qualifying PS2 points for NM_000546.6:c.665C>T (p.Pro222Leu/p.P222L). The governing Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for all three variant notations and contains no variant-specific entry; therefore PS2 cannot be evaluated from the available evidence.

VCEP rule

≥ 8 points ... 4-7 points ... 2-3 points ... 1 point

Evidence considered

• The case evidence documents the normalized variant as NM_000546.6:c.665C>T, NP_000537.3:p.(Pro222Leu)/p.(P222L), but provides no proband-parent trio result, de novo determination, or qualifying PS2 clinical point total.
• The VCEP Table-of-LFS-Cancers-and-Points-for-PS2-Code-Application.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L; no variant-specific entry was found.
• PMID:17724467 and PMID:19336573 report somatic/tumor observations of P222L, not a documented germline de novo observation with parental testing.

Still missing

• No documented de novo status or parental testing for the proband.
• No proband cancer phenotype and corresponding VCEP PS2 point assignment were provided.
• No variant-specific entry was found when Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L.

Sources

Reasoning

The TP53 VCEP PS4 points table governs this criterion and assigns 0.5 points for Revised Chompret clinical criteria, 1 point for Classic LFS criteria, and 0.5 points for HER2-positive breast cancer under age 40, with total-point thresholds of Supporting 1-1.5, Moderate 2-3.5, Strong 4-7.5, and Very Strong >=8. The available case evidence does not provide an affected proband phenotype, LFS clinical-criteria assessment, or a PS4 point total. Literature reviewed for PS4 includes PMID:17724467, which reports P222L in a diffuse large B-cell lymphoma sample with five somatic occurrences and zero germline occurrences in IARC, and PMID:19336573, which reports P222L in one BRCA1-related breast tumor; neither provides a VCEP-eligible germline LFS proband count or unaffected/population control comparison. PMID:12826609, PMID:17392385, and PMID:20065170 were also reviewed as PS4 candidate papers but do not provide variant-specific case-control or LFS proband evidence. Therefore PS4 cannot be assigned from the available evidence.

VCEP rule

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

Evidence considered

• PS4-Points-Table.pdf, PS4 Code Strength Based on Total Points: PS4_Supporting = 1-1.5, PS4_Moderate = 2-3.5, PS4 = 4-7.5, PS4_Very Strong >= 8.
• PS4-Points-Table.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L; no variant-specific row or pre-assigned code was found.
• PMID:17724467, Results/Table 1: P222L was reported in a diffuse large B-cell lymphoma sample, with five somatic occurrences and zero germline occurrences in the IARC database; this is not a germline LFS proband case-control comparison.
• PMID:19336573, Table 1, tumor sample B150: P222L (50%) was reported in a BRCA1-related breast tumor; the paper does not provide an unaffected/population control comparison or VCEP PS4 proband point assessment.
• PMID:12826609 was reviewed as a PS4 candidate but does not explicitly mention P222L or provide variant-specific case-control evidence.
• PMID:17392385 and PMID:20065170 were reviewed as PS4 candidates but do not mention the specific variant or provide variant-specific case-control evidence.

Still missing

• No affected-proband phenotype or LFS clinical-criteria data are available for NM_000546.6:c.665C>T.
• No PS4 point total can be calculated from the available case evidence.
• PS4-Points-Table.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L; no variant-specific entry was found.
• No eligible germline case-control comparison with affected-case and unaffected/population-control counts was identified in the reviewed papers.

Sources

Reasoning

The TP53 VCEP requires a different missense variant at the same amino-acid residue that was previously established as pathogenic or likely pathogenic under the TP53 VCEP specifications, without using PM5 for that prior classification; the VCEP also requires Grantham comparison and exclusion of splicing. The supplied evidence contains exact P222L reports but no qualifying different missense comparator at residue 222 with the required VCEP-established pathogenic or likely pathogenic status. The comparator candidate file contains zero same-residue candidates and reports a retrieval failure, so PM5 cannot be adjudicated from the available evidence.

VCEP rule

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. ... Missense variant at an amino acid residue where 1 different missense variant previously determined to be likely pathogenic according to the _TP53_ VCEP’s specifications has been seen before. **The previously seen likely pathogenic variant must have clinical data that demonstrates pathogenicity (i.e. PS2, PS4, PP1) in order for it to count towards PM5\_Supporting code application.**

Evidence considered

• TP53 VCEP PM5 rule requires a different missense variant at the same amino-acid residue previously determined to be pathogenic or likely pathogenic under the TP53 VCEP specifications, with the prior classification reached without PM5; Grantham comparison and splicing exclusion are also required.
• PMID:17724467 reports the assessed P222L variant itself, not a different residue-222 comparator, and does not establish a qualifying VCEP pathogenic or likely pathogenic comparator.
• PMID:19336573 reports the assessed P222L variant itself in Table 1, not a different residue-222 comparator.
• PM5 candidate collection reports zero same-residue candidates; its retrieval error prevents treating that collection as definitive evidence of absence.

Still missing

• A qualifying different TP53 missense comparator at residue 222, classified without PM5 under the TP53 VCEP specifications, is not available.

Sources

Reasoning

The TP53 VCEP requires documented cosegregation measured in meioses. The reviewed case evidence contains no affected relatives carrying NM_000546.6:c.665C>T, no unaffected relatives tested for the variant, no family structure, and no countable meioses. The governing Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L and has no variant-specific pre-assigned code. PP1 therefore cannot be assessed.

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

• No affected-relative or unaffected-relative genotype, pedigree, segregation result, or meiosis count for NM_000546.6:c.665C>T was present in the reviewed case evidence.
• The VCEP Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L; no variant-specific entry was found.
• PMID:17724467 and PMID:19336573 describe non-segregation-relevant somatic/tumor observations and do not provide family cosegregation data for this variant.

Still missing

• No familial genotypes or phenotype-linked relative testing are available.
• No family structure or countable meioses are available.
• No variant-specific entry was found when Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.665C>T, p.Pro222Leu, and p.P222L.

Sources

Reasoning

The TP53 VCEP rule for PP4 requires an observation of the variant with VAF 5-35% for Supporting, or at least two independent observations with VAF 5-25% for Moderate. The available evidence contains no VAF measurement for NM_000546.6:c.665C>T and no qualifying independent VAF observations. The variant-specific reports reviewed here are a somatic tumor report and a yeast functional study, neither of which supplies the VAF evidence required by this VCEP PP4 rule.

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

• The available case evidence does not report a VAF for c.665C>T/p.Pro222Leu/p.P222L.
• PMID:17724467 reports P222L in a yeast assay and does not provide a qualifying clinical VAF.
• PMID:19336573 reports P222L at an estimated 50% abundance in tumor sample B150, but this tumor abundance is not a qualifying VAF observation under the VCEP PP4 rule and does not establish the required independent observation design.

Still missing

• No VAF measurement is available for a qualifying observation of NM_000546.6:c.665C>T.
• No two independent observations with VAF 5-25% are available.

Sources

Reasoning

The TP53 VCEP BS2 rule requires documented unrelated females aged at least 60 years without cancer, all from one source, with strength determined by the count. The available evidence contains population allele counts and homozygote counts but does not document qualifying age, sex, cancer-free status, unrelatedness, or a single-source count. BS2 cannot therefore be evaluated.

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

• The available gnomAD records provide allele counts, ancestry frequencies, and homozygote counts, not the VCEP-required qualifying individual-level BS2 observations.
• No evidence was available establishing unrelated females aged ≥60 years without cancer from one source.

Still missing

• A single-source dataset documenting the number, sex, age, unrelatedness, and cancer-free status of qualifying individuals is required.

Sources

Reasoning

The TP53 VCEP defines BS4 as lack of segregation in affected family members diagnosed with LFS-associated cancers. The reviewed case evidence contains no affected-family-member genotypes, no family cancer histories linked to testing, and no documented non-segregation observation for NM_000546.6:c.665C>T (p.Pro222Leu/p.P222L). BS4 cannot be assessed.

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

• No affected-family-member genotype, LFS-associated cancer history linked to testing, or lack-of-segregation result for NM_000546.6:c.665C>T was present in the reviewed case evidence.
• The VCEP table defining LFS-associated cancers for this evidence group was searched for c.665C>T, p.Pro222Leu, and p.P222L; no variant-specific entry was found.
• The exact-variant papers reviewed (PMID:17724467 and PMID:19336573) do not report affected-family segregation or non-segregation data.

Still missing

• No affected family members with qualifying LFS-associated cancers were documented as tested.
• No discordant genotype-phenotype or other lack-of-segregation observation is available.

Sources