TP53 c.710T>C, p.Met237Thr

Reasoning

The TP53 VCEP PM2 rule applies at supporting strength when the allele frequency is less than 0.00003 (0.003%) in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group's frequency must be less than 0.00004. The current default all-comers gnomAD v4.1 data show total AF 1.2393524135768578e-06 (2/1,613,746 alleles), and the highest observed ancestry-group AF is Admixed American 1.667389201987528e-05 (1/59,974 alleles); homozygotes are 0. Both frequencies are below the VCEP thresholds, and no ancestry group has multiple observed alleles. 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%).

Evidence considered

• TP53 VCEP PM2 rule: apply at supporting strength below total AF 0.00003, with any ancestry group containing multiple alleles required to remain below AF 0.00004.
• gnomAD v4.1: total AF 1.2393524135768578e-06, 2/1,613,746 alleles, homozygotes 0; highest observed population Admixed American AF 1.667389201987528e-05, 1/59,974 alleles, homozygotes 0.
• gnomAD v2.1 and the available non-cancer subsets report the variant as absent; the VCEP does not require a non-cancer or exome-only source for these rules, so the current all-comers gnomAD v4.1 result is the governing population estimate.

Sources

Reasoning

The variant is a missense variant, NM_000546.6:c.710T>C (p.Met237Thr/p.M237T). The governing TP53 Supplementary Table S2 pre-assigns PP3_moderate for the exact coding change, with BayesDel class C65 and BayesDel score 0.516761. This direct VCEP table assignment governs and is consistent with the VCEP PP3 moderate missense rule requiring aGVGD class C65 and BayesDel score >= 0.16. The SpliceAI maximum delta score is 0.021, below the VCEP no-significant-splicing threshold of 0.2; this splice result is not used to create an additional PP3 assignment or double-counted. The governing flowchart was searched without an exact variant entry, and the single-amino-acid deletion spreadsheet was searched without an exact variant entry; neither gap overrides the exact pre-assigned S2 code.

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, matching row: c.710T>C | p.Met237Thr | Class C65 | BayesDel score 0.516761 | assigned code PP3_moderate | splice value 0.02.
• Case normalization identifies the variant as missense NM_000546.6:c.710T>C, NP_000537.3:p.(Met237Thr), also p.(M237T).
• SpliceAI result for this variant: DS_AG 0.0, DS_AL 0.021, DS_DG 0.0, DS_DL 0.0; maximum delta score 0.021.

Still missing

• No exact c.710T>C, p.Met237Thr, or p.M237T entry was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf.txt.
• No exact c.710T>C, p.Met237Thr, or p.M237T 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 PM1 moderate rule is limited to codons 175, 245, 248, 249, 273, and 282, or to a germline missense variant seen in cancerhotspots.org with at least 10 somatic occurrences for the same amino-acid change; the supporting rule requires 2-9 such occurrences. p.Met237Thr is at codon 237, outside the specified codons. The case evidence reports COSMIC occurrence count n=3 and a statistically significant hotspot, but it does not establish the VCEP-required cancerhotspots.org same-amino-acid occurrence route, and n=3 is not the VCEP moderate threshold of at least 10.

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

• The TP53 VCEP PM1 codon list is 175, 245, 248, 249, 273, and 282; the assessed variant is p.Met237Thr at codon 237.
• COSMIC reports COSV53037559 with 3 somatic occurrences for this variant.
• The hotspot evidence says the variant lies in a statistically significant hotspot, but does not provide a cancerhotspots.org same-amino-acid count meeting the VCEP threshold.

Sources

Reasoning

The TP53 VCEP BA1 rule requires a filtering allele frequency (FAF) of at least 0.001 (0.1%) in a single eligible gnomAD continental ancestry group, with at least 2,000 alleles tested and at least 2 variant alleles. The highest observed eligible-subpopulation frequency in gnomAD v4.1 is Admixed American AF 1.667389201987528e-05 (1/59,974 alleles), far below 0.001 and with only one variant allele; the total AF is 1.2393524135768578e-06 (2/1,613,746 alleles), with zero homozygotes. 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

• TP53 VCEP BA1 rule: FAF ≥ 0.001 or 0.1% in an eligible single-ancestry continental subpopulation, requiring ≥2,000 alleles tested and at least 2 alleles present.
• gnomAD v4.1: total AF 1.2393524135768578e-06, 2/1,613,746 alleles, homozygotes 0; highest observed population was Admixed American, AF 1.667389201987528e-05, 1/59,974 alleles, homozygotes 0.

Sources

Reasoning

The TP53 VCEP BS1 rule requires FAF at least 0.0003 but less than 0.001 in one eligible gnomAD continental ancestry group, with at least 2,000 alleles tested and at least 2 variant alleles. The highest observed eligible-subpopulation frequency in gnomAD v4.1 is Admixed American AF 1.667389201987528e-05 (1/59,974 alleles), below 0.0003 and not meeting the minimum two-allele requirement; total AF is 1.2393524135768578e-06 (2/1,613,746 alleles). 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

• TP53 VCEP BS1 rule: FAF ≥ 0.0003 but < 0.001 in an eligible single-ancestry continental subpopulation, requiring ≥2,000 alleles tested and at least 2 alleles present.
• gnomAD v4.1: highest observed population was Admixed American, AF 1.667389201987528e-05, 1/59,974 alleles, homozygotes 0; total AF 1.2393524135768578e-06, 2/1,613,746 alleles, homozygotes 0.

Sources

Reasoning

The variant is TP53 p.Met237Thr. The TP53 VCEP permits PS1 only when comparing with a variant asserted as pathogenic or likely pathogenic under the TP53 VCEP specifications, with no RNA or SpliceAI evidence of a splicing difference. The available case evidence does not establish a qualifying previously pathogenic or likely pathogenic variant with the same amino-acid change p.Met237Thr; ClinVar classifies the assessed variant as uncertain significance, and the available paper extracts do not provide a qualifying same-change classification.

VCEP rule

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. ... Can be applied to variants asserted as Pathogenic following the TP53 VCEP’s specifications. ... Can be applied to variants asserted as Likely Pathogenic following the TP53 VCEP’s specifications.

Evidence considered

• Variant: NM_000546.6:c.710T>C, NP_000537.3:p.(Met237Thr).
• ClinVar variation 481069 classifies the assessed variant as uncertain significance with seven clinical-laboratory submissions and no expert-panel submission.
• The available paper extracts do not identify a previously established pathogenic or likely pathogenic p.Met237Thr comparator.

Still missing

• A validated prior TP53 p.Met237Thr variant classified as pathogenic or likely pathogenic under the TP53 VCEP is not available.

Sources

Reasoning

The available case evidence contains no documented de novo observation, parental testing result, or proband-level LFS cancer point assignment for NM_000546.6:c.710T>C (p.Met237Thr/p.M237T). The governing VCEP rule assigns PS2 strength by de novo evidence points: Supporting at 1 point, Moderate at 2-3 points, Strong at 4-7 points, and Very Strong at >=8 points. The required VCEP file Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.710T>C, p.Met237Thr, and p.M237T; no variant entry was found, so no pre-assigned code overrides the rule. PS2 cannot be assessed from the supplied evidence.

VCEP rule

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

Evidence considered

• The case evidence bundle provides no de novo observation, parental testing result, or proband-level LFS cancer point assignment for NM_000546.6:c.710T>C.
• The VCEP table Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.710T>C, p.Met237Thr, and p.M237T; no matching variant entry was found.
• The VCEP CSPEC entry defines PS2 as Supporting for 1 point, Moderate for 2-3 points, Strong for 4-7 points, and Very Strong for >=8 points.

Still missing

• No documented de novo status or parental testing result for the variant.
• No proband-level LFS cancer point assignment is available.
• No entry for c.710T>C, p.Met237Thr, or p.M237T was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf after searching all three notations.

Sources

Reasoning

The TP53 VCEP Functional-worksheet.xlsx Supplementary Table S3 row for M237T records Kato as Partially functional, Funk as LOF, Giacomelli as noLOF, Kotler as noLOF, Kawaguchi as NA, and assigns the preliminary functional code No evidence. The VCEP functional flowchart requires Partially functional on Kato data plus LOF by the majority of other available assays for PS3_Moderate; the recorded assay pattern does not meet that rule, and the governing worksheet explicitly assigns No evidence rather than PS3. The searched Flowchart-for-application-of-functional-rule-codes.pdf contains no variant-specific M237T entry and only provides general pathways. Therefore PS3 is not assessed, not applied.

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 PS3\_Supporting may also be applied to small deletions that demonstrate LOF on the majority of available assays

Evidence considered

• Functional-worksheet.xlsx, Supplementary Table S3, row M237T: Kato class = Partially functional; Funk class = LOF; Giacomelli class = noLOF; Kotler class = noLOF; Kawaguchi class = NA; preliminary functional code = No evidence.
• Flowchart-for-application-of-functional-rule-codes.pdf, page 1: for missense variants with Kato data, Partially functional (Kato) plus LOF by the majority of available assays maps to PS3_Moderate; the M237T worksheet row does not satisfy this pathway and is pre-assigned No evidence.
• The Kato assay source (PMID:12826609) describes quantitative yeast-based transactivation testing of 2,314 TP53 missense mutants across eight p53-responsive promoters, but the extracted paper finding does not explicitly mention c.710T>C or p.M237T.

Still missing

• Functional-worksheet.xlsx was searched for c.710T>C, p.Met237Thr, p.M237T, and M237T; its exact M237T row assigns No evidence rather than a PS3 code.
• Flowchart-for-application-of-functional-rule-codes.pdf was searched for c.710T>C, p.Met237Thr, p.M237T, and M237T; it has no variant-specific entry and provides only general PS3/BS3 pathways.

Sources

Reasoning

The TP53 VCEP assigns PS4 from proband phenotype points: Revised Chompret 0.5 point, Classic LFS 1 point, or HER2-positive breast cancer diagnosed before age 40 0.5 point, with Supporting at 1-1.5 points, Moderate at 2-3.5, Strong at 4-7.5, and Very Strong at >=8. The available case evidence does not provide an affected proband's cancer phenotype, age, HER2 status, Revised Chompret status, Classic LFS status, or a case-control count/estimate. The PS4-Points-Table.pdf was searched for c.710T>C, p.Met237Thr, and p.M237T and contains no variant-specific entry. Literature_pass.json has no ai_classified_papers; the reviewed paper extracts do not provide variant-specific PS4 case-control or phenotype-point evidence. Therefore PS4 cannot be assigned.

VCEP rule

PS4_Supporting = 1-1.5 points PS4_Moderate = 2-3.5 points PS4 = 4-7.5 points PS4_Very Strong = >= 8 points

Evidence considered

• PS4-Points-Table.pdf: Clinical criteria Revised Chompret = 0.5 point, Classic LFS criteria = 1 point, and HER2+ breast cancer diagnosed before age 40 = 0.5 point; PS4_Supporting = 1-1.5 points, PS4_Moderate = 2-3.5 points, PS4 = 4-7.5 points, and PS4_Very Strong = >= 8 points.
• The consolidated case evidence provides no proband phenotype, cancer age, HER2 status, Chompret/Classic LFS designation, case-control counts, odds ratio, or confidence interval for this variant.
• The governing PS4 table was searched under c.710T>C, p.Met237Thr, and p.M237T; no variant-specific row was found.
• literature_pass.json lists PS4 candidate papers but ai_classified_papers is empty; available paper extracts provide no variant-specific PS4 case-control or phenotype evidence.

Still missing

• No affected-proband cancer phenotype, age, HER2 status, Revised Chompret status, or Classic LFS status is available.
• No case-control counts, odds ratio, or confidence interval for c.710T>C/p.Met237Thr/p.M237T are available.
• No entry for c.710T>C, p.Met237Thr, or p.M237T was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/TP53/fulltext/PS4-Points-Table.pdf.txt.
• literature_pass.json contains no ai_classified_papers; its PS4 candidate papers did not yield variant-specific PS4 evidence in the available paper extracts.

Sources

Reasoning

The TP53 VCEP PM5 rule requires a different missense variant at the same amino-acid residue that was classified as pathogenic or likely pathogenic under the TP53 VCEP specifications, with the prior classification reached without PM5; the VCEP also requires the assessed change to be chemically equal or more different by Grantham comparison and splicing to be excluded. The collected PM5 search found nine candidates but zero same-residue candidates, and the retrieval record reports an HTTP 429 failure, so the evidence does not establish whether a qualifying p.Met237 comparator exists.

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 known pathogenic residue in comparison to the wild type residue). Splicing should be ruled out with either RNA data or SpliceAI < 0.2.

Evidence considered

• The TP53 VCEP PM5 rule requires a different missense variant at the same amino-acid residue classified as pathogenic or likely pathogenic under the TP53 VCEP specifications, with the prior classification reached without PM5; it also requires Grantham comparison and splicing exclusion.
• pm5_candidates.json reports 9 total candidates, 0 same-residue candidates, and an HTTP 429 Too Many Requests retrieval error.

Still missing

• Complete a validated same-residue TP53 p.Met237 comparator search and confirm each comparator’s VCEP classification, classification without PM5, Grantham comparison, and splicing status.

Sources

Reasoning

The available case evidence contains no affected-relative genotypes, segregation results, family structure, or countable meioses for NM_000546.6:c.710T>C (p.Met237Thr/p.M237T). The VCEP requires cosegregation in 3-4 meioses for Supporting, 5-6 meioses for Moderate, or >=7 meioses across >1 family for Strong. The required VCEP file Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for all three variant notations and contained no matching variant entry; no pre-assigned PP1 code overrides the rule. PP1 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

• The case evidence bundle provides no affected-relative genotypes, segregation results, family structure, or countable meioses for this variant.
• The VCEP table Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched for c.710T>C, p.Met237Thr, and p.M237T; no matching variant entry was found.
• The VCEP PP1 rule requires cosegregation in 3-4 meioses for Supporting, 5-6 meioses for Moderate, or >=7 meioses across >1 family for Strong.

Still missing

• No family genotypes or affected-relative segregation results are documented.
• No countable meioses or number of families is documented.
• No entry for c.710T>C, p.Met237Thr, or p.M237T was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf after searching all three notations.

Sources

Reasoning

The TP53 VCEP PP4 rule is a low-variant-allele-fraction phenotype rule requiring 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 does not provide VAF, the required multigene-panel-testing context, blood-cancer status, or confirmation that the observation represents the VCEP's intended somatic-origin setting. The variant is not reported as meeting BA1 or BS1 in the available evidence, but the required VAF observations are absent. Therefore PP4 cannot be assessed.

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 TP53 VCEP PP4 Supporting rule requires: 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%).
• The TP53 VCEP PP4 Moderate rule requires: At least 2 independent observations of the variant with VAF 5-25%.
• No VAF or qualifying observation context is present in the available case evidence.

Still missing

• No VAF is reported for this variant.
• No confirmation is available that the variant was detected on multigene panel testing in the VCEP-required context.
• No information is available on blood-cancer status or confirmation of somatic origin.
• No independent VAF observations can be counted.

Sources

Reasoning

The TP53 VCEP BS2 rule requires 2-3, 4-7, or at least 8 unrelated females who have reached at least 60 years of age without cancer, all from one source, with older individuals diagnosed with sarcoma excluded. The supplied population data provide allele counts, frequencies, and homozygote counts but do not identify unrelated female carriers, ages, cancer-free status, source provenance, or sarcoma history. BS2 cannot be evaluated from the available evidence.

VCEP rule

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

• TP53 VCEP BS2 rule requires age, sex, unrelatedness, cancer-free status, single-source provenance, and sarcoma exclusion; gnomAD data supplied only allele and homozygote counts and do not provide these required individual-level facts.

Still missing

• Need a single-source cohort identifying unrelated female carriers aged ≥60, cancer-free status, and exclusion of sarcoma diagnosed at ≥61 years.

Sources

Reasoning

The TP53 VCEP Functional-worksheet.xlsx Supplementary Table S3 row for M237T records Kato as Partially functional, Funk as LOF, Giacomelli as noLOF, Kotler as noLOF, Kawaguchi as NA, and assigns the preliminary functional code No evidence. The VCEP functional flowchart requires Partially functional on Kato data plus noLOF by all available assays for BS3_Supporting, or Functional on Kato data plus noLOF by the majority of available assays for BS3. The M237T row satisfies neither pathway because Kato is not Functional and Funk is LOF; the governing worksheet assigns No evidence. The searched Flowchart-for-application-of-functional-rule-codes.pdf contains no variant-specific M237T entry and only provides general pathways. Therefore BS3 is not assessed, not applied.

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 BS3\_Supporting may also be applied to small deletions with available Kotler et al. data that are loss of function (LOF) by the majority of available assays

Evidence considered

• Functional-worksheet.xlsx, Supplementary Table S3, row M237T: Kato class = Partially functional; Funk class = LOF; Giacomelli class = noLOF; Kotler class = noLOF; Kawaguchi class = NA; preliminary functional code = No evidence.
• Flowchart-for-application-of-functional-rule-codes.pdf, page 1: Partially functional (Kato) plus noLOF by all available assays maps to BS3_Supporting, while Functional (Kato) plus noLOF by the majority maps to BS3; the M237T worksheet row does not satisfy either pathway.
• The Kato assay source (PMID:12826609) describes quantitative yeast-based transactivation testing of 2,314 TP53 missense mutants across eight p53-responsive promoters, but the extracted paper finding does not explicitly mention c.710T>C or p.M237T.

Still missing

• Functional-worksheet.xlsx was searched for c.710T>C, p.Met237Thr, p.M237T, and M237T; its exact M237T row assigns No evidence rather than a BS3 code.
• Flowchart-for-application-of-functional-rule-codes.pdf was searched for c.710T>C, p.Met237Thr, p.M237T, and M237T; it has no variant-specific entry and provides only general PS3/BS3 pathways.

Sources

Reasoning

The available case evidence contains no affected family members, family genotypes, or documented lack of segregation for NM_000546.6:c.710T>C (p.Met237Thr/p.M237T). The TP53 VCEP defines BS4 as strong evidence based on lack of segregation in affected family members diagnosed with LFS-associated cancers described in the governing table. The table was searched for all three variant notations and contained no matching variant entry. 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

• The case evidence bundle provides no affected-family non-segregation data for this variant.
• The TP53 VCEP BS4 rule requires lack of segregation in affected family members diagnosed with LFS-associated cancers described in Table of LFS Cancers and Points for PS2 and PP1 Code Application.
• The VCEP table was searched for c.710T>C, p.Met237Thr, and p.M237T; no matching variant entry was found.

Still missing

• No affected family members or family genotypes are documented.
• No lack-of-segregation observation is documented.
• No entry for c.710T>C, p.Met237Thr, or p.M237T was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf after searching all three notations.

Sources