PMS2 c.706-13T>C, p.?

Reasoning

The governing VCEP PM2 rule assigns supporting evidence for an allele frequency below 0.00002 in gnomAD v4. The gnomAD v4.1 total allele frequency for NM_000535.7:c.706-13T>C is 9.96589e-06 (15/1,505,134 alleles), with 0 homozygotes; this is below 0.00002, so PM2 is met at Supporting strength. No governing VCEP pilot-table entry was found for NM_000535.7:c.706-13T>C, c.706-13T>C, or p.? in VCEP-pilot-variants---MMR.xlsx.txt.

VCEP rule

Absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles ) in gnomAD v4 dataset

Evidence considered

• gnomAD v4.1: total AF 9.96589e-06 from 15 alternate alleles among 1,505,134 alleles, with 0 homozygotes; the highest subpopulation AF was 1.71686e-05 in Admixed American individuals.
• The VCEP pilot-variant table was searched for NM_000535.7:c.706-13T>C, c.706-13T>C, and p.?; no matching row was found.
• The total gnomAD v4.1 allele frequency is below the VCEP PM2 cutoff of 0.00002.

Still missing

• No matching entry for NM_000535.7:c.706-13T>C, c.706-13T>C, or p.? was found in VCEP-pilot-variants---MMR.xlsx.txt.

Sources

Reasoning

The variant is intronic, so the VCEP BP4 intronic/synonymous splice path applies. SpliceAI reports DS_AG 0.007, DS_AL 0.001, DS_DG 0.009, and DS_DL 0.000; the maximum delta score is 0.009, which is <=0.1 and therefore meets the VCEP no-splicing-impact threshold. The exact variant was not found in HCI-PRIORS-PMS2.txt.txt; that indexed table is limited to missense substitutions, while BP4 is independently met through the intronic SpliceAI path.

VCEP rule

For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.

Evidence considered

• SpliceAI result for NM_000535.7:c.706-13T>C: DS_AG=0.007, DS_AL=0.001, DS_DG=0.009, DS_DL=0.000; maximum delta score=0.009.
• The VCEP BP4 intronic/synonymous path requires SpliceAI to predict no splicing impact with delta score <=0.1.
• HCI-PRIORS-PMS2.txt.txt was searched for c.706-13T>C, p.?, and p.?; no exact entry was found.

Still missing

• No exact c.706-13T>C, p.?, or p.? entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PMS2/fulltext/HCI-PRIORS-PMS2.txt.txt; the indexed table is for missense substitutions, and the intronic SpliceAI path was available.

Sources

Reasoning

The variant is intronic at the non-canonical splice position c.706-13, so the applicable VCEP PP3 path is the SpliceAI splice-defect path, not the missense HCI-prior path. SpliceAI reports DS_AG 0.007, DS_AL 0.001, DS_DG 0.009, and DS_DL 0.000; the maximum delta score is 0.009, below the VCEP threshold of >=0.2. The exact variant was not found in HCI-PRIORS-PMS2.txt.txt, but that table is indexed for missense substitutions and is not applicable to this intronic variant.

VCEP rule

Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023.

Evidence considered

• SpliceAI result for NM_000535.7:c.706-13T>C: DS_AG=0.007, DS_AL=0.001, DS_DG=0.009, DS_DL=0.000; maximum delta score=0.009.
• The VCEP PP3 splice path requires a predicted splice defect at a non-canonical splicing nucleotide using SpliceAI with delta score >=0.2.
• HCI-PRIORS-PMS2.txt.txt was searched for c.706-13T>C, p.?, and p.?; no exact entry was found.

Still missing

• No exact c.706-13T>C, p.?, or p.? entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PMS2/fulltext/HCI-PRIORS-PMS2.txt.txt; the VCEP indexes that table for missense substitutions, not this intronic variant.

Sources

Reasoning

The governing VCEP BA1 rule requires a gnomAD v4 Grpmax filtering allele frequency of at least 0.0028 (0.28%) and exclusion as a founder pathogenic variant. The gnomAD v4.1 Grpmax filtering allele frequency is 7.49e-06 (0.000749%), which is below 0.0028; therefore BA1 is not met. No governing VCEP pilot-table entry was found for NM_000535.7:c.706-13T>C, c.706-13T>C, or p.? in VCEP-pilot-variants---MMR.xlsx.txt.

VCEP rule

GnomAD v4 Grpmax filtering allele frequency ≥ 0.0028 (0.28%) and variant is excluded as founder pathogenic variant.

Evidence considered

• gnomAD v4.1: 15/1,505,134 total alleles, total AF 9.96589e-06, 0 homozygotes, and Grpmax FAF 7.49e-06.
• The VCEP pilot-variant table was searched for NM_000535.7:c.706-13T>C, c.706-13T>C, and p.?; no matching row was found.
• Because the observed gnomAD v4.1 Grpmax FAF is below 0.0028, the frequency condition for BA1 is not satisfied.

Still missing

• No matching entry for NM_000535.7:c.706-13T>C, c.706-13T>C, or p.? was found in VCEP-pilot-variants---MMR.xlsx.txt.

Sources

Reasoning

The governing VCEP BS1 rule requires a gnomAD v4 Grpmax filtering allele frequency of at least 0.00028 and less than 0.0028 (0.028-0.28%) and exclusion as a founder pathogenic variant. The gnomAD v4.1 Grpmax filtering allele frequency is 7.49e-06 (0.000749%), below 0.00028; therefore BS1 is not met. No governing VCEP pilot-table entry was found for NM_000535.7:c.706-13T>C, c.706-13T>C, or p.? in VCEP-pilot-variants---MMR.xlsx.txt.

VCEP rule

GnomAD v4 Grpmax filtering allele frequency ≥ 0.00028 and < 0.0028 (0.028-0.28%) and variant is excluded as founder pathogenic variant.

Evidence considered

• gnomAD v4.1: Grpmax FAF 7.49e-06 (0.000749%), with 15 alternate alleles among 1,505,134 total alleles and 0 homozygotes.
• The VCEP pilot-variant table was searched for NM_000535.7:c.706-13T>C, c.706-13T>C, and p.?; no matching row was found.
• The observed Grpmax FAF is below the VCEP BS1 interval of 0.00028 to less than 0.0028.

Still missing

• No matching entry for NM_000535.7:c.706-13T>C, c.706-13T>C, or p.? was found in VCEP-pilot-variants---MMR.xlsx.txt.

Sources

Reasoning

PVS1 cannot be assigned from the available evidence. The variant is NM_000535.7:c.706-13T>C (NP_000526.2:p.?), an intronic non-canonical splice variant in exon 6i; the variant facts do not establish a null consequence, and no patient RNA assay demonstrating loss of full-length/reference transcript or a premature stop codon/in-frame functional-domain disruption is available. SpliceAI predicts no significant splice impact (maximum delta 0.009). The VCEP PVS1 rule provides full-strength evidence for nonsense/frameshift variants introducing a PTC at or before codon 798, large genomic alterations, canonical IVS±1/±2 variants with frame disruption and predicted NMD, or qualifying patient-mRNA evidence; none of those qualifying paths is established here. The PVS1 decision-tree file and VCEP pilot table were searched for c.706-13T>C and p.? without an entry for this variant.

VCEP rule

Nonsense/frameshift variant introducing Premature Termination Codon (PTC)^a ≤ codon 798 in _PMS2_. Refer to Appendix for details. ... Large genomic alterations^a of single or multi-exon size. ... Variants at IVS±1 or IVS±2**^a,c ** where exon skipping or use of a cryptic splice site disrupts reading frame and is predicted to undergo NMD. Not to be combined with PP3 and not to be used for a confirmed splice defect (see PVS1 for variants where patient mRNA assays indicate splicing aberration). If exon skipping or use of a cryptic splice site preserves reading frame and the altered region is critical to protein function^b then use PVS1_Strong. If exon skipping or use of a cryptic splice site disrupts reading frame and is NOT predicted to undergo NMD then use PVS1_Moderate. ... Variants where mRNA assays using RNA derived from patient constitutional biological samples indicate that the variant allele results in a splicing aberration (with evidence that the variant allele produces no full-length/reference transcript) leading to premature stop codon or in-frame deletion disrupting a functional domain^b or protein conformation. Splicing aberration must be confirmed in a minigene assay or an additional RNA assay from an independent laboratory if it is a non-canonical splice site variant.

Evidence considered

• NM_000535.7:c.706-13T>C is normalized as NP_000526.2:p.? and recorded as an intronic non-canonical splice variant in exon 6i; consequence class is unknown.
• SpliceAI Lookup reports maximum delta score 0.009 and predicts no significant splice impact.
• The VCEP PVS1 rule covers nonsense/frameshift PTCs at or before codon 798 in PMS2, large genomic alterations, canonical IVS±1/±2 variants with qualifying frame/NMD consequences, and qualifying patient-mRNA splicing aberration; the available evidence establishes none of these paths.
• PVS1_DecisionTree_MMR.pdf.txt and VCEP-pilot-variants---MMR.xlsx.txt were searched for c.706-13T>C and p.?; neither contains this variant.

Still missing

• No entry for NM_000535.7:c.706-13T>C or p.? was found in PVS1_DecisionTree_MMR.pdf.txt.
• No entry for NM_000535.7:c.706-13T>C or p.? was found in VCEP-pilot-variants---MMR.xlsx.txt.
• A patient-derived RNA assay confirming or excluding aberrant splicing and the resulting transcript/protein consequence is not available.

Sources

Reasoning

The VCEP permits PS1 Strong when a variant affects the same non-canonical splice nucleotide as a confirmed Pathogenic splice variant with similar or worse SpliceAI prediction, or PS1 Moderate for a Likely Pathogenic comparator. The case identifies NM_000535.7:c.706-13T>C with protein consequence NP_000526.2:p.? and SpliceAI max delta 0.009, but provides no confirmed Pathogenic or Likely Pathogenic comparator at c.706-13 or a same-amino-acid missense comparator. The available ClinVar record is not an expert-panel assertion and is not evidence for the required VCEP comparator. Therefore the rule cannot be evaluated from the available evidence.

VCEP rule

A predicted missense substitution that encodes the same amino acid change with a different underlying nucleotide change previously established by this VCEP as Pathogenic (not a predicted or confirmed splice defect). ... OR ... Variants affecting the same non-canonical splice nucleotide as a confirmed Pathogenic splice variant with similar or worse splicing in silico prediction using SpliceAI.

Evidence considered

• The normalized consequence is NM_000535.7:c.706-13T>C with NP_000526.2:p.?.
• SpliceAI reports DS_AG 0.007, DS_AL 0.001, DS_DG 0.009, DS_DL 0.0, with max delta score 0.009.
• ClinVar variation 182812 contains no expert-panel submission and reports non-expert submissions as benign or likely benign, so it does not establish the VCEP Pathogenic or Likely Pathogenic comparator required by PS1.
• No matching c.706-13T>C or p.? entry was found in the governing PMS2 full-text directory search.

Still missing

• No confirmed Pathogenic or Likely Pathogenic VCEP comparator variant at c.706-13 was identified in the available evidence.
• No protein-level amino-acid change is available because the variant is annotated as NP_000526.2:p.?.

Sources

Reasoning

The available case evidence contains no documented proband de novo observation, parental testing result, confirmed maternity/paternity, or de novo point assignment for NM_000535.7:c.706-13T>C; therefore the VCEP's de novo-point thresholds cannot be evaluated.

VCEP rule

≥ 4 de novo points = Very Strong; 2–3.5 de novo points = Strong; 1–1.5 de novo points = Moderate; 0.5 de novo points = Supporting.

Evidence considered

• The case evidence contains no case-specific proband, parental-testing, parentage, or de novo observation for NM_000535.7:c.706-13T>C.

Still missing

• Documented proband genotype and phenotype
• Both parental genotypes and confirmed maternity/paternity
• VCEP de novo point assignment

Reasoning

The VCEP permits PS3 from calibrated functional assays or, at Moderate strength, an MMR function defect established by the functional-assay flowchart. The case evidence contains no variant-specific functional assay result, RNA assay result, functional odds, or flowchart outcome for PMS2 NM_000535.7:c.706-13T>C (NP_000526.2:p.?). The governing assay documentation lists validated assay designs, controls, thresholds, and proposed strengths, but contains no entry for c.706-13T>C or p.?. The functional-assay flowchart text likewise contains no variant-specific result. Therefore PS3 cannot be evaluated from the available VCEP-governed evidence.

Evidence considered

• ClinGen InSiGHT PMS2 specification v2.0, PS3: calibrated functional assays with functional odds for pathogenicity >18.7 support Strong; functional odds >4.3 and <=18.7, an MMR function defect following the functional assay flowchart, or complete monoallelic loss of expression support Moderate; calibrated functional odds >2.08 and <=4.3 support Supporting.
• Functional-assay-SVI-documentation-MMR.xlsx, sheet 'MMR assays': validated MMR assay categories, control requirements, assay thresholds, and proposed evidence strengths are listed, but no row identifies PMS2 c.706-13T>C or p.?.
• Functional-assay-flowchart.pdf: the extracted flowchart provides general pathways for splice-site/intronic variants and functional assays, but no row or result identifies PMS2 c.706-13T>C or p.?.
• The case evidence reports SpliceAI max delta score 0.009 (reported as 0.01), which is an in-silico prediction and not a functional assay result; it was not used for PS3.

Still missing

• No entry for c.706-13T>C was found in Functional-assay-SVI-documentation-MMR.xlsx.txt.
• No entry for NP_000526.2:p.? or p.? was found in Functional-assay-SVI-documentation-MMR.xlsx.txt.
• No entry for c.706-13T>C was found in Functional-assay-flowchart.pdf.txt.
• No entry for NP_000526.2:p.? or p.? was found in Functional-assay-flowchart.pdf.txt.
• A variant-specific calibrated assay result, functional odds, or appropriately performed RNA/protein functional study is required to assess PS3.

Sources

Reasoning

The PMS2 VCEP specifies PM3 using a point-based framework for evidence of the variant in trans with another pathogenic allele in affected probands, but the available case evidence documents no affected proband observation, second pathogenic PMS2 variant, phase determination, or PM3 point total for NM_000535.7:c.706-13T>C. Therefore PM3 cannot be assigned.

VCEP rule

PM3 point-based rule: Very Strong >= 4 points; Strong 2 - 3.5 points; Moderate 1 - 1.5 points; Supporting = 0.5 points.

Evidence considered

• The PMS2 VCEP PM3 criterion is point-based: Very Strong requires >=4 points, Strong requires 2-3.5 points, Moderate requires 1-1.5 points, and Supporting requires 0.5 points.
• The consolidated case evidence contains no documented affected proband with this variant, no co-occurring pathogenic PMS2 variant, no cis/trans phase result, and no PM3 point assignment.

Still missing

• Affected-proband observations consistent with the relevant PMS2 inheritance context.
• A co-occurring pathogenic PMS2 variant and evidence that it is in trans with NM_000535.7:c.706-13T>C.
• Per-proband evidence sufficient to calculate the VCEP PM3 points.

Sources

Reasoning

The available case evidence provides no affected or unaffected relatives, pedigree-level genotype/phenotype observations, meioses, or combined Bayes Likelihood Ratio for NM_000535.7:c.706-13T>C; the VCEP PP1 thresholds therefore cannot be evaluated.

VCEP rule

Combined Bayes Likelihood Ratio >18.7 in ≥2 families = Strong; >4.3 and ≤18.7 = Moderate; >2.08 and ≤4.3 = Supporting.

Evidence considered

• The case evidence contains no variant-specific family segregation data, informative meioses, or combined Bayes Likelihood Ratio.

Still missing

• Pedigree with disease status and variant status for informative relatives
• Number of informative meioses and family count
• Combined Bayes Likelihood Ratio

Reasoning

The VCEP PP4 rule requires qualifying CRC or endometrial MSI-H tumor evidence and/or MMR protein loss consistent with PMS2. The available case evidence does not provide a patient tumor count, MSI result, tumor-genome result, or PMS2-consistent IHC result. The required VCEP reference files were searched: Table-for-CMMRD-diagnosis.pdf.txt contains only the general CMMRD scoring table and no c.706-13T>C or p.? entry; VCEP-pilot-variants---MMR.xlsx.txt contains no c.706-13T>C or p.? entry. PP4 cannot be evaluated without the required phenotype/tumor data.

Evidence considered

• The VCEP PP4 rule requires one, two, or at least three independent CRC/endometrial MSI-H tumors, respectively, with the specified standard panel or tumor genome and/or MMR protein loss consistent with the variant location.
• Table-for-CMMRD-diagnosis.pdf.txt was searched for c.706-13T>C and p.?; no variant entry was found, while the table provides only general CMMRD scoring criteria.
• VCEP-pilot-variants---MMR.xlsx.txt was searched for c.706-13T>C and p.?; no matching row was found.

Still missing

• Patient-specific CRC/endometrial MSI-H tumor count and testing method are unavailable.
• Patient-specific PMS2-consistent MMR protein-loss or tumor-genome result is unavailable.
• No c.706-13T>C or p.? entry was found in Table-for-CMMRD-diagnosis.pdf.txt.
• No c.706-13T>C or p.? entry was found in VCEP-pilot-variants---MMR.xlsx.txt.
• CMMRD clinical features and score cannot be assessed from the available case evidence.

Sources

Reasoning

The governing VCEP BS2 rule requires documented in-trans co-occurrence with a known pathogenic sequence variant in the same gene in a patient meeting the specified colorectal or other Lynch-syndrome cancer age condition, absence of CMMRD manifestations, and confirmation of phase through parental or offspring testing. The available case evidence contains no such co-occurrence, phase, age-at-diagnosis, or CMMRD documentation, so BS2 cannot be evaluated.

VCEP rule

Co-occurrence in trans with a known pathogenic sequence variant in the same gene in a patient with colorectal cancer after age 45 (or other LS cancer above the median age of onset for that cancer in LS), and who has no previous or current evidence of clinical manifestations of CMMRD as per Aronson et al 2022 (Refer to 'Table for CMMRD diagnosis.pdf'). Confirmation of phase requires testing of parents or offspring.

Evidence considered

• The available case evidence does not document a qualifying patient with this variant and a known pathogenic PMS2 variant in trans, nor phase confirmation or the required clinical details.

Still missing

• No documented in-trans co-occurrence with a known pathogenic PMS2 variant.
• No parental or offspring testing confirming phase.
• No qualifying cancer age or CMMRD clinical assessment for a co-occurring individual.

Sources

Reasoning

The VCEP permits BS3 from calibrated functional assays with functional odds for pathogenicity <=0.05 or >0.05 and <=0.48, and from variant-specific proficient function in protein and mRNA-based assays following the MMR functional-assay flowchart. For synonymous or intronic variants, Strong BS3 also requires no associated mRNA aberration determined with nonsense-mediated decay inhibition. The case evidence contains no variant-specific functional assay result, functional odds, RNA assay result, or demonstrated proficient protein/mRNA function for PMS2 NM_000535.7:c.706-13T>C (NP_000526.2:p.?). The two governing VCEP functional files contain no entry for this variant under c.706-13T>C or p.?. Therefore BS3 cannot be evaluated.

Evidence considered

• ClinGen InSiGHT PMS2 specification v2.0, BS3: calibrated functional assays with functional odds for pathogenicity <=0.05 support Strong, and odds >0.05 and <=0.48 support Supporting; variant-specific proficient protein and mRNA function following the MMR functional-assay flowchart supports Supporting.
• Functional-assay-SVI-documentation-MMR.xlsx, sheet 'MMR assays': validated assay categories, controls, thresholds, and proposed evidence strengths are listed, but no row identifies PMS2 c.706-13T>C or p.?.
• Functional-assay-flowchart.pdf: the extracted flowchart provides general criteria for proficient versus deficient function, but no variant-specific result identifies PMS2 c.706-13T>C or p.?.
• The case evidence reports SpliceAI max delta score 0.009 (reported as 0.01), which is an in-silico prediction and not evidence of proficient function; it was not used for BS3.

Still missing

• No entry for c.706-13T>C was found in Functional-assay-SVI-documentation-MMR.xlsx.txt.
• No entry for NP_000526.2:p.? or p.? was found in Functional-assay-SVI-documentation-MMR.xlsx.txt.
• No entry for c.706-13T>C was found in Functional-assay-flowchart.pdf.txt.
• No entry for NP_000526.2:p.? or p.? was found in Functional-assay-flowchart.pdf.txt.
• A variant-specific calibrated benign functional result, proficient protein/mRNA assay, or NMD-inhibited RNA assay showing no aberration is required to assess BS3.

Sources

Reasoning

The available case evidence provides no unaffected carrier observations, pedigree-level lack-of-segregation data, informative meioses, or combined Bayes Likelihood Ratio for NM_000535.7:c.706-13T>C; the VCEP BS4 thresholds therefore cannot be evaluated.

VCEP rule

Combined Bayes Likelihood Ratio <0.05 = Strong; >0.05 and ≤0.48 = Supporting.

Evidence considered

• The case evidence contains no variant-specific non-segregation observations, informative meioses, or combined Bayes Likelihood Ratio.

Still missing

• Pedigree with disease status and variant status for informative relatives
• Unaffected carriers or other documented non-segregation observations
• Combined Bayes Likelihood Ratio

Reasoning

BP5 is applicable under the PMS2 VCEP, but the case evidence contains no patient-specific tumor results showing MSS or absent MMR protein loss, no inconsistent LS-spectrum MMR loss, and no BRAF V600E or MLH1 methylation result. The criterion cannot be assessed without those data.

Evidence considered

• The VCEP BP5 rule requires 2 or 3 qualifying tumors for supporting evidence or at least 4 qualifying tumors for strong evidence, or the specified BRAF V600E/MLH1 methylation findings; none are documented in the available case evidence.

Still missing

• Patient-specific tumor MSS/MSI results and MMR protein-expression findings are unavailable.
• Patient-specific BRAF V600E or MLH1 methylation results are unavailable.
• The number of qualifying tumors is unavailable.

Sources