PMS2 c.1145-11C>T, p.?

Reasoning

The variant is an intronic non-canonical splice-region variant, so the PMS2 VCEP splice-impact branch applies. SpliceAI reports a maximum delta score of 0.213 for NM_000535.7:c.1145-11C>T. The governing PMS2 VCEP specification assigns PP3_Supporting for a predicted splice defect at a non-canonical splice nucleotide with SpliceAI delta score >= 0.2; therefore PP3 is met at Supporting strength. The HCI-PRIORS-PMS2.txt.txt table was searched for c.1145-11C>T, p.?, and p.? and has no exact entry; that missense-only lookup is not needed because the VCEP splice rule directly governs this intronic variant.

Rule

Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as specified by the PMS2 VCEP.

Evidence considered

• The PMS2 VCEP specification states that PP3_Supporting applies to a predicted splice defect at a non-canonical splice nucleotide when SpliceAI delta score is >= 0.2.
• SpliceAI reports DS_AL 0.213 as the maximum delta score for NM_000535.7:c.1145-11C>T, with the predicted acceptor-loss event at a non-canonical intronic position.
• The indexed HCI-PRIORS-PMS2.txt.txt file is a missense-only lookup table and was searched under c.1145-11C>T, p.?, and p.? without an exact entry.

Still missing

• No exact c.1145-11C>T, p.?, or p.? entry was found in HCI-PRIORS-PMS2.txt.txt; the file is indexed for missense variants, while this variant is intronic.

Sources

Reasoning

The governing InSiGHT PMS2 VCEP specifies BS1 Strong for gnomAD v4 Grpmax filtering allele frequency >=0.00028 and <0.0028 (0.028-0.28%), provided the variant is not a founder pathogenic variant. The gnomAD v4.1 joint Grpmax FAF is 0.00072958 (0.072958%), which lies within this interval. No founder designation is present in the available evidence; BS1 Strong is met.

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

• The InSiGHT PMS2 VCEP Version 2.0 defines BS1 Strong as gnomAD v4 Grpmax filtering allele frequency >=0.00028 and <0.0028 (0.028-0.28%), excluding founder pathogenic variants.
• gnomAD v4.1 reports joint Grpmax FAF 0.00072958 (0.072958%), based on 99/1,558,792 total alleles and 0 homozygotes; the South Asian subgroup has AF 0.000887134 (80/90,178 alleles).

Sources

Reasoning

The variant is intronic at c.1145-11, which is at or beyond -21 relative to the exon boundary and therefore falls within the PMS2 VCEP BP7 scope of intronic variants at or beyond -21/+7. The VCEP assigns BP7_Supporting to such variants; BP7 is met at Supporting strength. This criterion is applied from variant location and is not an additional use of the SpliceAI prediction.

Rule

A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic) satisfies BP7_Supporting under the PMS2 VCEP.

Evidence considered

• The PMS2 VCEP BP7 rule applies at Supporting strength to synonymous or intronic variants at or beyond -21/+7 relative to the exonic boundary.
• NM_000535.7:c.1145-11C>T is an intronic variant located 11 bases upstream of the exon boundary, within the specified BP7 range.

Sources

Reasoning

The applicable PMS2-specific InSiGHT VCEP Version 2.0 framework recognizes PVS1 at the canonical IVS ±1 or ±2 splice sites when exon skipping or cryptic splice use disrupts the reading frame and is predicted to undergo NMD. NM_000535.7:c.1145-11C>T is an intronic position 11 bases upstream of the exon boundary, not a canonical ±1/2 splice-site variant; its predicted protein consequence is p.? and no patient RNA assay demonstrating a null transcript or NMD-triggering aberrant transcript is available. SpliceAI reports a max delta score of 0.213, which indicates a possible non-canonical splice impact but does not establish the VCEP PVS1 requirements. Therefore PVS1 is not met under the governing PMS2 VCEP framework.

Rule

PMS2 InSiGHT VCEP Version 2.0 PVS1: canonical IVS ±1/2 splice variants qualify for full strength only when exon skipping or cryptic splice use disrupts the reading frame and is predicted to undergo NMD.

Evidence considered

• The PMS2 InSiGHT VCEP Version 2.0 PVS1 rule specifies canonical IVS ±1/2 splice variants with reading-frame disruption and predicted NMD for the full-strength splice-site pathway.
• VariantValidator maps NM_000535.7:c.1145-11C>T to intronic position −11 with predicted protein consequence NP_000526.2:p.? and no exon annotation for a protein-altering consequence.
• SpliceAI scores are DS_AG 0.01, DS_AL 0.213, DS_DG 0.018, and DS_DL 0.003; max delta is 0.213, indicating possible splice impact but not proving a PVS1-qualifying null transcript or NMD outcome.

Still missing

• No patient-derived RNA evidence establishes aberrant splicing that produces a premature stop codon or qualifying in-frame deletion.
• No demonstrated exon-skipping or cryptic-splice outcome establishes reading-frame disruption and NMD.
• Variant-level exon annotation and protein consequence remain unresolved beyond p.?

Sources

Reasoning

The governing InSiGHT PMS2 VCEP specifies PM2 Supporting when the allele frequency is <0.00002 (<1 in 50,000 alleles) in gnomAD v4. The gnomAD v4.1 all-comers total AF is 0.0000635107 (99/1,558,792 alleles), above the VCEP threshold, and the non-cancer datasets also do not establish absence: v2.1 non-cancer exomes AF 0.000136764 (31/226,668) and v3.1 non-cancer genomes AF 0.0000338094 (5/147,888). Therefore PM2 is not met.

Rule

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

Evidence considered

• The InSiGHT PMS2 VCEP Version 2.0 defines PM2 Supporting as absent or allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.
• gnomAD v4.1 all-comers reports AF 0.0000635107 (99/1,558,792 alleles), with 0 homozygotes; its highest population AF is South Asian at 0.000887134 (80/90,178 alleles).
• For the available non-cancer subsets, gnomAD v2.1 non-cancer exomes reports AF 0.000136764 (31/226,668 alleles; homozygotes 0), and gnomAD v3.1 non-cancer genomes reports AF 0.0000338094 (5/147,888 alleles; homozygotes 0).

Sources

Reasoning

The governing InSiGHT PMS2 VCEP specifies BA1 at gnomAD v4 Grpmax filtering allele frequency >=0.0028 (0.28%), with exclusion of a founder pathogenic variant. The gnomAD v4.1 joint Grpmax FAF is 0.00072958 (0.072958%), below 0.0028; therefore BA1 is not met. No founder designation is needed to change this frequency-based conclusion.

Rule

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

Evidence considered

• The InSiGHT PMS2 VCEP Version 2.0 defines BA1 as gnomAD v4 Grpmax filtering allele frequency >=0.0028 (0.28%) and excludes founder pathogenic variants.
• gnomAD v4.1 reports joint Grpmax FAF 0.00072958 (0.072958%), with the highest observed population frequency in South Asian individuals at 0.000887134 (80/90,178 alleles; homozygotes 0).

Sources

Reasoning

The variant is an intronic non-canonical splice-region variant, for which the PMS2 VCEP BP4 rule requires SpliceAI to predict no splicing impact with delta score <= 0.1. The observed SpliceAI maximum delta score is 0.213, which exceeds that cutoff; therefore BP4 is not met. The HCI-PRIORS-PMS2.txt.txt table was searched for c.1145-11C>T, p.?, and p.? and has no exact entry; it is indexed for missense variants and does not override the applicable intronic SpliceAI rule.

Rule

For intronic and synonymous variants, SpliceAI predicts no splicing impact with delta score <= 0.1 as specified by the PMS2 VCEP.

Evidence considered

• The PMS2 VCEP specification requires SpliceAI delta score <= 0.1 for BP4 in intronic and synonymous variants.
• SpliceAI reports a maximum delta score of 0.213 for NM_000535.7:c.1145-11C>T, above the VCEP BP4 cutoff.
• The indexed HCI-PRIORS-PMS2.txt.txt file is a missense-only lookup table and was searched under c.1145-11C>T, p.?, and p.? without an exact entry.

Still missing

• No exact c.1145-11C>T, p.?, or p.? entry was found in HCI-PRIORS-PMS2.txt.txt; the file is indexed for missense variants, while this variant is intronic.

Sources

Reasoning

The PMS2 VCEP permits PS1 for a variant affecting the same non-canonical splice nucleotide as a confirmed Pathogenic or Likely Pathogenic splice variant, provided the new variant has a similar or worse SpliceAI prediction. This variant is intronic, has an unknown protein consequence (NP_000526.2:p.?), and has SpliceAI maximum delta 0.213, but the available evidence does not document a qualifying comparator at the same splice nucleotide or its SpliceAI score. Therefore PS1 cannot be adjudicated from the available evidence.

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. The analogous Likely Pathogenic rule requires PM2_supporting for the missense pathway.

Evidence considered

• The PMS2 VCEP PS1 rule includes variants affecting the same non-canonical splice nucleotide as a confirmed Pathogenic splice variant with similar or worse SpliceAI prediction, or the analogous Likely Pathogenic rule.
• The case variant is NM_000535.7:c.1145-11C>T with protein consequence NP_000526.2:p.? and SpliceAI maximum delta score 0.213.
• No qualifying same-nucleotide Pathogenic or Likely Pathogenic comparator and comparator SpliceAI score are documented in the available case evidence.

Still missing

• A confirmed Pathogenic or Likely Pathogenic comparator affecting the same non-canonical splice nucleotide, with its SpliceAI prediction, is needed.

Sources

Reasoning

The PMS2 InSiGHT VCEP specifies PS2 using de novo points: 2 points per proband when both maternity and paternity are confirmed and the proband has an LS-spectrum tumor with MMR-deficient tumor data consistent with the affected gene; 1 point when both parents are confirmed but tumor MSI/IHC/methylation data are unavailable; and 0.5 points for assumed de novo status with maternity and/or paternity unconfirmed. The available case evidence contains no proband-level de novo observation, parental testing results, maternity or paternity confirmation, tumor phenotype data, or de novo point calculation for NM_000535.7:c.1145-11C>T, so PS2 cannot be assigned.

Rule

Proband with a de novo variant with both maternity and paternity confirmed in a case with MMR deficient LS spectrum tumor consistent with the affected gene: 2 points per proband; or both parents confirmed with an LS-spectrum tumor but no tumor MSI/IHC/methylation data: 1 point per proband; or assumed de novo with maternity and/or paternity unconfirmed and an LS-spectrum tumor: 0.5 points per proband. PS2 Very Strong requires >=4 de novo points, Strong 2-3.5, Moderate 1-1.5, Supporting 0.5.

Evidence considered

• The PMS2 InSiGHT VCEP PS2 rule assigns 2 de novo points per proband with confirmed maternity and paternity plus an MMR-deficient LS-spectrum tumor consistent with the affected gene, 1 point with confirmed parents but no tumor data, and 0.5 points when maternity and/or paternity are unconfirmed.
• No proband-level de novo, parental-testing, tumor-consistency, or de novo-point evidence was present for this variant.

Still missing

• Document the proband's LS-spectrum phenotype and tumor MSI/IHC/methylation findings, if available.
• Document testing of both biological parents and whether maternity and paternity are confirmed.
• Calculate the applicable VCEP de novo points per proband and across probands.

Sources

Reasoning

The ClinGen InSiGHT PMS2 Version 2.0 specification requires calibrated functional odds, an MMR function defect established through the functional-assay flowchart, or qualifying monoallelic-expression evidence for PS3. No variant-specific protein-function assay, MMR activity assay, or RNA assay is reported for NM_000535.7:c.1145-11C>T. SpliceAI predicts a possible splice effect with a maximum delta score of 0.213, but this is computational prediction rather than functional evidence and cannot satisfy PS3. The available literature extraction contains only general ACMG guidance and no assay result for this variant.

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

• The ClinGen InSiGHT PMS2 Version 2.0 rule permits PS3 Strong only for calibrated functional assays with functional odds for pathogenicity >18.7, PS3 Moderate for odds >4.3 and <=18.7 or a qualifying MMR function defect/complete loss of variant-allele expression, and PS3 Supporting for odds >2.08 and <=4.3.
• The PMS2 functional assay flowchart directs variants with predicted splicing impact to splicing assays; no variant-specific splicing assay result is present.
• SpliceAI reports DS_AL 0.213 as the maximum delta score, which is a computational splice-impact prediction and not an experimental functional assay.
• The extracted literature includes general guidance that splice-site impact requires RNA or protein confirmation, but does not report a PMS2 c.1145-11C>T assay result.

Still missing

• Variant-specific RNA splicing analysis with appropriate controls and nonsense-mediated-decay considerations is unavailable.
• Variant-specific calibrated protein or MMR activity assay with assay controls and a validated functional odds estimate is unavailable.

Sources

Reasoning

The PMS2 VCEP defines PM3 for co-occurrence of the evaluated variant with a known pathogenic or likely pathogenic PMS2 variant in a patient with clinical features consistent with CMMRD. A pathogenic/likely pathogenic partner variant, affected-proband observation, and phase are not documented for this case, so no PM3 points can be assigned; the VCEP point thresholds are 0.5 for Supporting, 1–1.5 for Moderate, 2–3.5 for Strong, and ≥4 for Very Strong.

Rule

Co-occurrence with a known pathogenic/likely pathogenic sequence variant in the same gene in a patient with clinical features consistent with CMMRD; pathogenic/likely pathogenic in trans = 1.0 point, phase unknown = 0.5 points; sum all cases. Strength: Supporting = 0.5 points, Moderate = 1–1.5 points, Strong = 2–3.5 points, Very Strong = ≥4 points.

Evidence considered

• The PMS2 VCEP PM3 rule requires co-occurrence with a known pathogenic or likely pathogenic variant in the same gene in a patient with clinical features consistent with CMMRD.
• The PMS2 VCEP assigns 1.0 point for a pathogenic/likely pathogenic variant in trans and 0.5 points when phase is unknown; no qualifying partner observation or phase information is documented here.

Still missing

• Affected-proband clinical features consistent with CMMRD are not documented.
• A known pathogenic or likely pathogenic PMS2 partner variant is not documented.
• Phase of the evaluated variant relative to any partner variant is not documented.

Sources

Reasoning

The PMS2 InSiGHT VCEP requires co-segregation evidence evaluated with a combined Bayes Likelihood Ratio: greater than 18.7 for PP1 Strong in at least two families, greater than 4.3 through 18.7 for PP1 Moderate, and greater than 2.08 through 4.3 for PP1 Supporting. No affected-relative genotypes, unaffected-relative genotypes, pedigree structure, meioses, family count, or calculated Bayes Likelihood Ratio is documented for this variant, so PP1 cannot be assigned.

Rule

Co-segregation with disease in pedigree(s) with a 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 PMS2 InSiGHT VCEP PP1 thresholds are combined Bayes Likelihood Ratio >18.7 for Strong, >4.3 to <=18.7 for Moderate, and >2.08 to <=4.3 for Supporting.
• No segregation pedigree, relative testing, informative meiosis count, family count, or Bayes Likelihood Ratio was present for this variant.

Still missing

• Provide pedigrees identifying affected and unaffected relatives and their phenotype status.
• Provide variant testing results for informative relatives and the number of informative meioses.
• Calculate the combined Bayes Likelihood Ratio across families using the VCEP-recommended segregation method.

Sources

Reasoning

PP4 is applicable under the InSiGHT PMS2 specification, requiring one or more CRC/endometrial MSI-H tumors or tumor-genome evidence and/or MMR protein loss consistent with the variant location. The case evidence contains no patient-specific tumor MSI, tumor-genome, or PMS2 IHC result, so no PP4 strength can be assigned.

Rule

Supporting: 1 CRC/endometrial MSI-H tumor using a standard panel of 5-10 markers or tumor genome and/or loss of MMR protein expression consistent with the variant location; Moderate: 2 independent tumors; Strong: at least 3 independent tumors in at least 2 families. MSI-H tumor with inconsistent protein expression does not meet PP4.

Evidence considered

• The governing InSiGHT PMS2 Version 2.0 PP4 rule requires one CRC/endometrial MSI-H tumor with a standard marker panel or tumor genome and/or MMR protein loss consistent with the variant location; the available case evidence does not report such patient-specific findings.

Still missing

• Patient-specific tumor MSI result using the specified marker panel or tumor genome result
• Patient-specific MMR immunohistochemistry result with loss consistent with PMS2 variant location
• Tumor independence and family information if multiple tumors are used

Sources

Reasoning

The governing InSiGHT PMS2 VCEP restricts BS2 Strong to documented in-trans co-occurrence with a known pathogenic sequence variant in the same gene in an appropriately aged Lynch-syndrome cancer patient without clinical manifestations of CMMRD, with phase confirmation by parental or offspring testing. The available case evidence contains no such patient-level co-occurrence, phase, age, or CMMRD assessment, so BS2 cannot be evaluated.

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; confirmation of phase requires testing of parents or offspring.

Evidence considered

• The InSiGHT PMS2 VCEP Version 2.0 requires BS2 Strong for in-trans co-occurrence with a known pathogenic sequence variant in PMS2 in a qualifying patient, plus phase confirmation by parents or offspring and no clinical manifestations of CMMRD.
• The available case evidence provides population allele counts and frequencies but does not provide a qualifying patient-level co-occurrence or the required phase, age, and CMMRD information.

Still missing

• A qualifying patient-level co-occurrence with a known pathogenic PMS2 variant is not documented.
• Phase confirmation, cancer age, and absence of CMMRD manifestations are not documented.

Sources

Reasoning

The ClinGen InSiGHT PMS2 Version 2.0 specification requires calibrated functional odds <=0.05 for BS3 Strong, calibrated odds >0.05 and <=0.48 for BS3 Supporting, or variant-specific proficient protein and mRNA-based laboratory results under the MMR functional assay flowchart. No variant-specific benign/proficient protein assay, MMR activity assay, or RNA assay is reported for NM_000535.7:c.1145-11C>T. The SpliceAI maximum delta score of 0.213 is a computational prediction and cannot establish normal splicing or proficient function. Therefore BS3 cannot be assigned.

Rule

Calibrated functional assays with functional odds for pathogenicity <=0.05 OR synonymous substitutions and intronic variants with no associated mRNA aberration 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. BS3 Supporting: calibrated functional assays with functional odds for pathogenicity >0.05 and <=0.48 OR variant-specific proficient function in protein and mRNA-based lab assays as per MMR functional assay flowchart.

Evidence considered

• The ClinGen InSiGHT PMS2 Version 2.0 rule permits BS3 Strong for calibrated functional odds for pathogenicity <=0.05 or qualifying normal mRNA findings, and BS3 Supporting for calibrated odds >0.05 and <=0.48 or variant-specific proficient protein and mRNA-based assays.
• The PMS2 functional assay flowchart requires variant-specific assay evidence to classify proficient versus deficient MMR function; no such result is available for this variant.
• SpliceAI reports DS_AL 0.213 as the maximum delta score, which cannot establish normal splicing or proficient function because it is not an experimental assay.
• The extracted literature provides only general methodological guidance and no variant-specific benign functional result.

Still missing

• Variant-specific RNA assay demonstrating no mRNA aberration, including appropriate nonsense-mediated-decay inhibition where applicable, is unavailable.
• Variant-specific protein-function or MMR activity assay demonstrating proficient function with validated controls is unavailable.

Sources

Reasoning

The PMS2 InSiGHT VCEP requires lack of co-segregation to be evaluated using a combined Bayes Likelihood Ratio, with BS4 Strong below 0.05 and BS4 Supporting greater than 0.05 through 0.48. No affected-family-member non-segregation observations, phenotype assessments, informative meioses, pedigree data, or combined Bayes Likelihood Ratio is documented for this variant. Therefore, BS4 cannot be assigned; absence of segregation data is not evidence of non-segregation.

Rule

Lack of co-segregation with disease in pedigree(s) with a combined Bayes Likelihood Ratio <0.05: Strong; >0.05 and <=0.48: Supporting.

Evidence considered

• The PMS2 InSiGHT VCEP BS4 thresholds are combined Bayes Likelihood Ratio <0.05 for Strong and >0.05 to <=0.48 for Supporting.
• No affected-relative non-segregation, informative meiosis, pedigree, or Bayes Likelihood Ratio evidence was present for this variant; missing segregation data were not treated as non-segregation.

Still missing

• Provide pedigrees and phenotype assessments for affected relatives tested for the variant.
• Provide variant results for informative affected and unaffected relatives and the number of informative meioses.
• Calculate the combined Bayes Likelihood Ratio for lack of co-segregation across pedigrees.

Sources

Reasoning

BP5 is applicable under the InSiGHT PMS2 specification when there are alternate-molecular-basis findings: at least 2 tumors for supporting or at least 4 tumors for strong evidence, or the specified BRAF V600E/MLH1 methylation findings. The case evidence does not report tumor MSS/IHC, inconsistent MMR loss, BRAF V600E, or MLH1 methylation results, so BP5 cannot be assigned.

Rule

Supporting: 2 or 3 tumors with MSS and/or no loss of MMR protein expression and/or inconsistent MMR protein loss, or 1 specified BRAF V600E/MLH1 methylation finding; Strong: at least 4 tumors or at least 2 specified BRAF V600E/MLH1 methylation findings.

Evidence considered

• The governing InSiGHT PMS2 Version 2.0 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 finding; none is reported in the available case evidence.

Still missing

• Patient-specific tumor MSS and MMR-protein-expression results
• Patient-specific BRAF V600E or MLH1 methylation result where applicable
• Number and independence of qualifying tumors

Sources