MSH2 c.942+3A>T, p.?

Reasoning

PS3 is met at Moderate strength under the MSH2 VCEP functional-assay flowchart. This is a non-canonical splice-site variant, and multiple variant-specific RNA studies demonstrate a splice defect: c.942+3A>T causes MSH2 exon 5 skipping, produces an exon-5-deficient transcript, and yields an in-frame 50-amino-acid deletion. The 16395668 study used endogenous lymphoblastoid-cell RNA with and without puromycin and found the skipped transcript at high levels in the carrier versus nearly undetectable levels in controls; PMID:19267393 also evaluated this variant by lymphoblastoid-cell RNA/cDNA analysis and reported exon deletion. Under the flowchart, a splice-site variant with complete impact demonstrated by patient-derived RNA is classified as deficient function. The VCEP functional-assay documentation and flowchart were searched for the exact variant notations c.942+3A>T and p.?; neither file contains a variant-specific pre-assigned code, so the VCEP flowchart branch governs rather than a calibrated functional-odds value.

VCEP rule

Calibrated functional assays with functional odds for pathogenicity >4.3 and <= 18.7 OR MMR function defect following functional assay flowchart* OR Variants with monoallelic expression: complete loss of expression (<10% of wild-type in cDNA without puromycin) of the variant allele. Full-length transcript should be analysed with and without NMD block.

Evidence considered

• Functional-assay-flowchart.pdf, page 1: for splice-site, silent, or intronic variants, the splicing-assay branch classifies complete impact with patient-derived RNA assays as deficient function.
• Functional-assay-SVI-documentation-MMR.xlsx, sheet 'MMR assays': the approved full-length-transcript assay uses patient leukocyte RNA with active/inhibited NMD and detects allelic loss at <=10%; this table contains no row for c.942+3A>T or p.?.
• PMID:10978353: the paper states that A>T at nt942+3 interferes with the MSH2 exon 5 donor-splicing mechanism and leads to mRNA lacking exon 5.
• PMID:16395668, Table 1 family 5073 and Results: endogenous lymphoblastoid-cell RT-PCR with and without puromycin identified MSH2 exon 5 skipping; the skipped transcript was high in the carrier and nearly undetectable in controls, and exon 5 loss produces an in-frame 50-amino-acid deletion.
• PMID:19267393: variant-specific lymphoblastoid-cell RNA/cDNA analysis associated MSH2 c.942+3A>T with exon deletion; the tumor showed MSI-H with loss of MSH2/MSH6 expression.
• PMID:19419416: independently reports c.942+3A>T as abnormal splicing with an in-frame deletion of exon 5 encoding loss of residues 265-314.

Still missing

• No exact-variant entry for c.942+3A>T or p.? was found in Functional-assay-SVI-documentation-MMR.xlsx.txt.
• No exact-variant entry for c.942+3A>T or p.? was found in Functional-assay-flowchart.pdf.txt.
• A calibrated functional odds value for this variant is not available; PS3 is therefore based on the VCEP MMR functional assay flowchart rather than calibrated odds.
• The available studies establish abnormal splicing but do not provide a variant-specific calibrated odds estimate from one of the VCEP-approved calibrated assays.

Sources

Reasoning

The variant is an intronic non-canonical splice-site variant at c.942+3. The governing VCEP PP3 rule permits Supporting evidence for a predicted splice defect at a non-canonical splicing nucleotide when SpliceAI delta score is >= 0.2. SpliceAI reports a maximum delta score of 0.486, which meets that threshold. The governing HCI missense-prior table was searched for c.942+3A>T and p.? and contains no matching entry; its missense path is not applicable to this intronic variant. The SpliceAI result is the sole computational evidence applied here; the same result is not counted as an additional independent predictor.

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 Lookup for NM_000251.3:c.942+3A>T: maximum delta score 0.486 (acceptor/donor component fields were not separately populated in the case evidence).
• ClinGen InSiGHT MSH2 VCEP v2.0 PP3 rule: the non-canonical splice-nucleotide path requires SpliceAI delta score >= 0.2; 0.486 meets it.
• HCI-PRIORS-MSH2.txt.txt was searched for c.942+3A>T and p.?; no matching entry was found, and the file declares a missense-only HCI prior lookup path.

Still missing

• No matching c.942+3A>T or p.? entry was found in HCI-PRIORS-MSH2.txt.txt; the HCI table's missense-prior path therefore cannot be applied.

Sources

Reasoning

The VCEP Supporting rule requires one CRC/Endometrial MSI-H tumor with standard MSI markers or tumor genome and/or MMR protein loss consistent with the variant location. PMID:19267393 reports an affected colorectal-cancer proband with an MSI-H tumor and loss of MSH2/MSH6 expression; PMID:16203774 independently reports a colorectal-cancer proband with MSI-high tumor and absent MSH2/MSH6 expression. MSH2 loss is consistent with an MSH2 variant under the VCEP instructions. The governing reference files were searched: Table-for-CMMRD-diagnosis.pdf.txt and VCEP-pilot-variants---MMR.xlsx.txt contain no entry for c.942+3A>T or p.?.

VCEP rule

1 CRC/Endometrial MSI-H tumor using a standard panel of 5-10 markers^e or tumor genome ​**and/or**​ loss of MMR protein expression consistent with the variant location. MSI-H tumor with inconsistent protein expression does not meet PP4.

Evidence considered

• PMID:19267393, Materials and Methods, Tumor Characteristics; Results, Database and Literature Search and Variant Interpretation: "MSH2 c.942+3A>T (MSI-H and MSH2/MSH6 loss)." The experimental context was colorectal-cancer proband tumor MSI/IHC testing.
• PMID:16203774, Results, Mutation analyses of population-based probands; Table 2, proband 122: the variant was identified in a colorectal-cancer proband whose tumor was MSI-high with absent MSH2 and MSH6 protein expression.
• The VCEP instruction states that MSH2 and MSH6 loss is consistent with an MSH2 pathogenic variant; this variant is an intronic MSH2 variant with protein consequence p.? in the normalized record.

Still missing

• No entry for c.942+3A>T or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/MSH2/fulltext/Table-for-CMMRD-diagnosis.pdf.txt.
• No entry for c.942+3A>T or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/MSH2/fulltext/VCEP-pilot-variants---MMR.xlsx.txt.

Sources

Reasoning

Expert panel International Society for Gastrointestinal Hereditary Tumours (InSiGHT) classified as Pathogenic.

VCEP rule

This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.

Evidence considered

• The VCEP CSPEC marks PP5 "Not Applicable for this VCEP" and states: "This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee."
• ClinVar expert panel classification

Sources

Reasoning

The MSH2 VCEP PM2 rule requires an allele frequency <0.00002 in gnomAD v4. gnomAD v4.1 reports this variant at AF 0.00267657 (31/11582 alleles), with Grpmax FAF 0.00234998; both the overall frequency and the maximum population frequency are far above the VCEP PM2 threshold. PM2 is not met.

VCEP rule

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

Evidence considered

• VCEP PM2 rule: Absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 dataset.
• gnomAD v4.1: total AF 0.00267657 (31/11582 alleles), Grpmax FAF 0.00234998, and zero homozygotes.
• The governing file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no matching entry was found.

Still missing

• The VCEP pilot-variant file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no entry for this variant was found.

Sources

Reasoning

The MSH2 VCEP BA1 rule requires a gnomAD v4 Grpmax filtering allele frequency ≥0.001 and that the variant be excluded as a founder pathogenic variant. gnomAD v4.1 reports a Grpmax FAF of 0.00234998, satisfying the frequency component, but the exact variant is described in the literature as a previously identified founder mutation. Because the founder-exclusion condition is not satisfied, BA1 is not met.

VCEP rule

GnomAD v4 Grpmax filtering allele frequency ≥ 0.001 (0.1%) and variant is excluded as founder pathogenic variant.

Evidence considered

• VCEP BA1 rule: GnomAD v4 Grpmax filtering allele frequency ≥ 0.001 (0.1%) and variant is excluded as founder pathogenic variant.
• gnomAD v4.1: total AF 0.00267657 (31/11582 alleles), Grpmax FAF 0.00234998, and zero homozygotes.
• PMID:16203774, Results and Table 2: the exact variant is identified as a previously identified founder mutation in MSH2.
• The governing file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no matching entry was found.

Still missing

• The VCEP pilot-variant file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no entry for this variant was found.

Sources

Reasoning

The MSH2 VCEP BS1 rule requires a gnomAD v4 Grpmax filtering allele frequency ≥0.0001 and <0.001 and exclusion as a founder pathogenic variant. gnomAD v4.1 reports a Grpmax FAF of 0.00234998, which is above the rule's upper limit, and the exact variant is reported as a founder mutation. BS1 is therefore not met.

VCEP rule

GnomAD v4 Grpmax filtering allele frequency ≥ 0.0001 and < 0.001 (0.01-0.1%) and variant is excluded as founder pathogenic variant.

Evidence considered

• VCEP BS1 rule: GnomAD v4 Grpmax filtering allele frequency ≥ 0.0001 and < 0.001 (0.01-0.1%) and variant is excluded as founder pathogenic variant.
• gnomAD v4.1: Grpmax FAF is 0.00234998, above the BS1 interval; total AF is 0.00267657 (31/11582 alleles).
• PMID:16203774, Results and Table 2: the exact variant is identified as a previously identified founder mutation in MSH2.
• The governing file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no matching entry was found.

Still missing

• The VCEP pilot-variant file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no entry for this variant was found.

Sources

Reasoning

BS3 is not met because variant-specific functional evidence demonstrates abnormal rather than proficient MSH2 splicing. The VCEP flowchart directs splice-site variants to splicing assays, and the available patient-derived RNA studies consistently show exon 5 skipping or exon 5 deletion for c.942+3A>T. This directly conflicts with both VCEP BS3 paths: no calibrated functional odds for pathogenicity <=0.05 are available, and the variant does not show proficient function or absence of an mRNA aberration. The VCEP functional-assay documentation and flowchart were searched for c.942+3A>T and p.?; neither contains a variant-specific pre-assigned code.

VCEP rule

Calibrated functional assays with functional odds for Pathogenicity <= 0.05 OR Synonymous substitutions and intronic variants with no associated mRNA aberration (either splicing or allelic imbalance) as determined by laboratory assays conducted with nonsense-mediated decay inhibition. Whenever abnormal transcripts are identified at similar levels in controls they will be considered naturally occurring isoforms and not mRNA aberrations.

Evidence considered

• Functional-assay-flowchart.pdf, page 1: the splice-site branch requires a splicing assay; no-impact results can support proficient function only when the assay shows no mRNA impact, which is not the observed result.
• PMID:10978353: c.942+3A>T is reported to interfere with exon 5 donor splicing and produce mRNA lacking exon 5.
• PMID:16395668: patient-derived lymphoblastoid RNA showed MSH2 exon 5 skipping, with high skipped-transcript levels in the carrier and nearly undetectable levels in controls.
• PMID:19267393: variant-specific cDNA analysis associated c.942+3A>T with exon deletion.
• PMID:19419416: the variant is reported to cause abnormal splicing and an in-frame deletion of exon 5.

Still missing

• No exact-variant entry for c.942+3A>T or p.? was found in Functional-assay-SVI-documentation-MMR.xlsx.txt.
• No exact-variant entry for c.942+3A>T or p.? was found in Functional-assay-flowchart.pdf.txt.
• No calibrated functional odds value for this variant is available.

Sources

Reasoning

The variant is an intronic variant, so the VCEP BP4 intronic/synonymous path is within scope. That path requires SpliceAI to predict no splicing impact with delta score <= 0.1. SpliceAI reports a maximum delta score of 0.486, which is above the no-impact cutoff; therefore BP4 is not met. The HCI missense-prior path was also searched but is outside scope for this intronic variant and has no matching c.942+3A>T or p.? entry.

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 Lookup for NM_000251.3:c.942+3A>T: maximum delta score 0.486.
• ClinGen InSiGHT MSH2 VCEP v2.0 BP4 rule for intronic/synonymous variants requires delta score <= 0.1 for no predicted splicing impact; 0.486 does not meet that requirement.
• HCI-PRIORS-MSH2.txt.txt was searched for c.942+3A>T and p.?; no matching entry was found, and its declared lookup path is limited to missense substitutions.

Still missing

• No matching c.942+3A>T or p.? entry was found in HCI-PRIORS-MSH2.txt.txt; the HCI table's missense-prior path is not applicable to this intronic variant.

Sources

Reasoning

The VCEP governs PVS1 for variants with patient-derived RNA showing a splicing aberration, no full-length/reference transcript, and either a premature stop codon or an in-frame deletion disrupting a functional domain or protein conformation; for a non-canonical splice site, confirmation in a minigene assay or an additional independent RNA assay is required. MSH2 c.942+3A>T is a non-canonical intronic splice-site variant in intron 5, and independent RNA studies report exon 5 skipping and an in-frame 50-amino-acid deletion (PMID:16395668; PMID:19267393), with the variant also reported as producing an exon-5-skipped transcript (PMID:10978353). However, the extracted evidence does not establish that the variant allele produces no full-length/reference transcript or that the 50-amino-acid deletion disrupts a functional domain or protein conformation. Therefore the VCEP PVS1 rule cannot be fully evaluated and PVS1 is not assessed; no downgrade to strong or moderate is assigned because the required qualifying path is unresolved.

VCEP rule

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

• VCEP PVS1 rule: variants with patient constitutional RNA showing a splicing aberration, no full-length/reference transcript, and a premature stop codon or in-frame deletion disrupting a functional domain or protein conformation qualify; non-canonical splice-site variants require confirmation in a minigene assay or an additional independent RNA assay.
• The VCEP PVS1 decision-tree file specifies full PVS1 for GT-AG ±1/±2 splice variants only when exon skipping or cryptic splicing disrupts the reading frame and is predicted to undergo NMD; c.942+3A>T is non-canonical, so the patient-RNA branch of the CSPEC rule is the relevant path.
• PMID:16395668 reports the exact variant in family 5073; endogenous lymphoblastoid-cell RNA analysis with and without puromycin showed MSH2 exon 5 skipping, and the extracted finding states that exon 5 loss produces an in-frame deletion of 50 amino acids.
• PMID:19267393 reports the exact variant and evaluated lymphoblastoid-cell-line RNA/cDNA splicing after cycloheximide treatment; the extracted finding reports an association with exon deletion.
• PMID:10978353 reports the exact variant as interfering with the exon 5 donor-splicing mechanism and leading to mRNA lacking exon 5, but does not by itself establish absent full-length transcript or functional-domain/protein-conformation disruption.
• PMID:19419416 reports the exact variant as causing abnormal splicing with an in-frame deletion of exon 5 and a protein lacking residues 265–314; it does not establish the additional functional-disruption elements required by the VCEP PVS1 rule.
• The exact variant was searched in PVS1_DecisionTree_MMR.pdf.txt and VCEP-pilot-variants---MMR.xlsx.txt under c.942+3A>T and p.?; neither file contains a matching variant row.

Still missing

• Patient-derived RNA evidence that the variant allele produces no full-length/reference transcript is not explicitly documented in the extracted findings.
• Evidence that the 50-amino-acid exon 5 deletion disrupts a functional domain or protein conformation is not documented in the governing evidence reviewed.
• No matching entry for c.942+3A>T or p.? was found in PVS1_DecisionTree_MMR.pdf.txt.
• No matching entry for c.942+3A>T or p.? was found in VCEP-pilot-variants---MMR.xlsx.txt.

Sources

Reasoning

The variant is a non-canonical intronic splice-site variant (NP_000242.1:p.?), not a predicted missense substitution. SpliceAI predicts a maximum delta score of 0.486, and the literature documents exon 5 skipping, but no different variant affecting the same non-canonical nucleotide with an established Pathogenic or Likely Pathogenic classification was identified in the reviewed evidence. Therefore, the VCEP's same-nucleotide splice route cannot be evaluated without a qualifying comparator; the exact variant's own Pathogenic classification cannot serve as a self-comparator.

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). ... 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 protein consequence is NP_000242.1:p.?, and the variant is intronic c.942+3A>T rather than a predicted missense substitution.
• SpliceAI reported DS_AL 0.418, DS_DL 0.486, and maximum delta score 0.486 for NM_000251.3:c.942+3A>T.
• PMID:10978353 reports that A→T at nt942+3 interferes with exon 5 donor splicing and produces mRNA lacking exon 5.
• PMID:16395668 reports c.942+3A>T/c.94213a4t with MSH2 exon 5 skipping in lymphoblastoid-cell RNA analysis.
• PMID:19267393 and PMID:19419416 document the exact variant and abnormal splicing, but neither provides a qualifying different variant at the same non-canonical nucleotide for the PS1 comparator route.
• The exact variant is Pathogenic in an expert-panel ClinVar record, but using that same record as its own PS1 comparator would not satisfy the VCEP's different-variant requirement.

Still missing

• No different variant at the same non-canonical nucleotide, c.942+3, with a VCEP-established Pathogenic or Likely Pathogenic splice classification was identified in the reviewed evidence.
• MMR-Functional-domains.pdf.txt was searched for c.942+3A>T, p.?, and p.?; no variant-specific entry was found (this file governs PM1, not PS1).

Sources

Reasoning

The VCEP PS2 rule assigns evidence by de novo points per qualifying proband. PMID:10978353 reports that the recurrent c.942+3A>T variant arose de novo on multiple occasions in a haplotype analysis of 10 HNPCC families, but the available evidence does not identify a specific qualifying proband with the parentage confirmation and Lynch syndrome-spectrum tumor evidence required to assign points. PS2 is therefore not assessed.

VCEP rule

≥ 4 _de novo_ points ... OR ... 2 - 3.5 _de novo_ points ... OR ... 1 - 1.5 _de novo_ points ... OR ... 0.5 _de novo_ points

Evidence considered

• The VCEP PS2 entry assigns Very Strong for >=4 de novo points, Strong for 2-3.5 points, Moderate for 1-1.5 points, and Supporting for 0.5 de novo points.
• PMID:10978353 analyzed 42 members from 10 HNPCC families and concluded from haplotype analysis that the recurrent c.942+3A>T mutation arose de novo on multiple occasions; it does not provide a specific qualifying proband with the required parentage and tumor documentation.

Still missing

• A specific proband with c.942+3A>T and qualifying maternity and paternity confirmation is not identified.
• The required Lynch syndrome-spectrum tumor evidence for a qualifying proband is not documented.
• No de novo point total can therefore be calculated.

Sources

Reasoning

The VCEP specifies PM3 using a point-based framework: ≥ 4 points is Very Strong, 2 - 3.5 points is Strong, 1 - 1.5 points is Moderate, and = 0.5 points is Supporting. The available evidence reports affected probands and families carrying MSH2 c.942+3A>T, but does not document a second known pathogenic MSH2 variant in the same patient, confirmed trans phase, or sufficient affected-proband observations to assign PM3 points. Therefore PM3 cannot be assessed from the available evidence.

VCEP rule

≥ 4 points ... 2 - 3.5 points ... 1 - 1.5 points ... = 0.5 points

Evidence considered

• VCEP PM3 rule: ≥ 4 points = Very Strong, 2 - 3.5 points = Strong, 1 - 1.5 points = Moderate, and = 0.5 points = Supporting.
• The literature reports this exact variant in HNPCC/Lynch syndrome families and affected probands, including a 42-member analysis of 10 HNPCC families, a Newfoundland family cohort, and individual colorectal-cancer probands; these reports do not document a second pathogenic MSH2 variant in trans with confirmed phase.
• PMID:10978353 reports the exact variant across 10 HNPCC families and discusses family segregation and recurrent/de novo origin, but does not establish a second pathogenic MSH2 allele in trans.
• PMID:12352241 evaluates affected and at-risk members in 12 families carrying the exact variant, but the extracted evidence does not report a second MSH2 pathogenic variant or confirmed trans phase.
• PMID:16203774 reports one colorectal-cancer proband carrying the exact variant; no second MSH2 variant or phase information is reported in the extracted finding.
• PMID:19267393 reports a colorectal-cancer proband with the exact variant and tumor MSI-H/MSH2-MSH6 loss, plus splicing analysis; the extracted finding does not document biallelic MSH2 status or phase.

Still missing

• A patient-level second pathogenic or likely pathogenic MSH2 variant is not documented.
• Phase with any second MSH2 variant is not documented by parental or offspring testing.
• No VCEP PM3 point assignment can be made from the available affected-proband observations.

Sources

Reasoning

The VCEP PP1 rule requires a combined Bayes Likelihood Ratio greater than 18.7 in at least 2 families for Strong, greater than 4.3 and at most 18.7 for Moderate, or greater than 2.08 and at most 4.3 for Supporting. PMID:12352241 reports 12 families carrying the exact variant with testing of individuals at 50% risk, and PMID:10978353 reports segregation data from 10 HNPCC families, but no combined Bayes Likelihood Ratio or sufficient pedigree-level counts are available to calculate one. PP1 is therefore not assessed.

VCEP rule

Co-segregation with disease in pedigree(s) with a combined\* Bayes Likelihood Ratio^f >18.7​ in ≥2 families. ... OR ... Co-segregation with disease in pedigree(s) with a combined\* Bayes Likelihood Ratio^f >4.3 & ≤18.7. ... OR ... Co-segregation with disease in pedigree(s) with a combined\* Bayes Likelihood Ratio^f >2.08 & ≤4.3.

Evidence considered

• The VCEP PP1 thresholds are combined Bayes Likelihood Ratio >18.7 in at least 2 families for Strong, >4.3 and <=18.7 for Moderate, and >2.08 and <=4.3 for Supporting.
• PMID:12352241 studied 12 Newfoundland families with the specific MSH2 c.942+3A>T founder mutation, offered testing to individuals at 50% risk, and reviewed cancer type, age at onset, and age at death; it does not report a combined Bayes Likelihood Ratio.
• PMID:10978353 analyzed 42 members from 10 HNPCC families using family segregation data; the extracted evidence does not report a combined Bayes Likelihood Ratio.

Still missing

• A combined Bayes Likelihood Ratio is not reported.
• Pedigree-level affected/unaffected genotype and phenotype data needed to calculate the combined value are unavailable.

Sources

Reasoning

The MSH2 VCEP BS2 rule requires documented co-occurrence in trans with a known pathogenic sequence variant in the same gene in a patient meeting the specified age and clinical conditions, with phase confirmed through parental or offspring testing. The available evidence does not document such a co-occurrence, confirmed trans phase, or the required clinical context, so BS2 cannot be assessed.

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

• VCEP BS2 rule requires co-occurrence in trans with a known pathogenic sequence variant in the same gene, the specified clinical context, no previous or current evidence of CMMRD, and parental or offspring testing to confirm phase.
• The reviewed exact-variant reports describe single-variant observations and do not document a qualifying second pathogenic MSH2 allele in trans or confirmed phase.
• The governing file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no matching entry was found.

Still missing

• No patient-level co-occurring known pathogenic MSH2 sequence variant is documented.
• No confirmed trans phase by parental or offspring testing is documented.
• The required colorectal-cancer or other Lynch-syndrome cancer age and absence of CMMRD manifestations are not documented for a qualifying co-occurrence.
• The VCEP pilot-variant file VCEP-pilot-variants---MMR.xlsx was searched for c.942+3A>T, p.?, and related 942+3/94213 notation; no entry for this variant was found.

Sources

Reasoning

The VCEP BS4 rule requires lack of cosegregation with a combined Bayes Likelihood Ratio below 0.05 for Strong or greater than 0.05 and at most 0.48 for Supporting. The available family evidence describes carriers and affected or at-risk relatives but provides no non-segregating pedigree analysis or combined Bayes Likelihood Ratio. BS4 is therefore not assessed.

VCEP rule

Lack of co-segregation with disease in pedigree(s) with a combined\* Bayes Likelihood Ratio^f <0.05​. ... OR ... Lack of co-segregation with disease in pedigree(s) with a combined\* Bayes Likelihood Ratio^f >0.05 & ≤0.48.

Evidence considered

• The VCEP BS4 thresholds are combined Bayes Likelihood Ratio <0.05 for Strong and >0.05 and <=0.48 for Supporting.
• No source in the available case evidence supplies a non-segregating pedigree or a combined Bayes Likelihood Ratio for this variant.

Still missing

• A pedigree demonstrating lack of cosegregation is not available.
• A combined Bayes Likelihood Ratio is not reported.

Sources

Reasoning

The VCEP BP5 rule requires either 2 or 3 qualifying tumors with MSS, no MMR-protein loss, or inconsistent LS-spectrum protein loss, or one qualifying BRAF V600E/MLH1-methylated tumor. The available variant-specific evidence instead documents MSI-H tumors with MSH2/MSH6 loss and does not establish any qualifying BP5 tumor or BRAF/MLH1-methylation finding. Thus the criterion cannot be evaluated from the available evidence.

VCEP rule

2 or 3 tumors: CRC/Endometrial tumors with MSS and/or no loss of MMR protein expression and/or LS spectrum tumors^d with loss of MMR protein(s) that is inconsistent with the gene demonstrating genetic variation. OR 1 BRAF V600E (Colon only)/_MLH1_ methylation (in LS spectrum tumor only) with MSI-H/_MLH1_ loss.

Evidence considered

• The available variant-specific tumor reports describe MSI-H status with MSH2/MSH6 loss, which does not document the BP5 Supporting alternatives of 2 or 3 MSS/no-loss or inconsistent-loss tumors, or one BRAF V600E/MLH1-methylated tumor.
• No BRAF V600E or MLH1 methylation result was reported in the reviewed extracts for this variant.

Still missing

• No qualifying BP5 tumor count with MSS, no MMR-protein loss, inconsistent LS-spectrum loss, BRAF V600E, or MLH1 methylation is available.

Sources