MSH3 c.495A>G, p.(Lys165=)

Reasoning

No governing MSH3 VCEP or gene-specific framework was available, so the supplied generic PM2 supporting threshold of allele frequency <=0.0001 was used. The gnomAD v4.1 overall AF is 4.77112e-05 and its highest observed population AF is 6.27113e-05; the gnomAD v2.1 non-cancer exome AF is 1.68873e-05 and the gnomAD v3.1 non-cancer genome AF is 1.35177e-05. All reported frequencies are below 0.0001, with 0 homozygotes in each dataset, so PM2 is met at supporting strength.

Rule

Generic PM2: allele frequency <=0.0001, applied at supporting strength; no applicable VCEP specification was available.

Evidence considered

• Generic PM2 supporting threshold: allele frequency <=0.0001 (ClinGen SVI recommendation, PMID:25741868).
• gnomAD v4.1 reports overall AF 4.77112e-05 and maximum observed population AF 6.27113e-05 in European non-Finnish individuals, with 0 homozygotes.
• gnomAD v2.1 non-cancer exomes report AF 1.68873e-05 (4/236864 alleles) and 0 homozygotes; gnomAD v3.1 non-cancer genomes report AF 1.35177e-05 (2/147954 alleles) and 0 homozygotes.
• The variant is a synonymous MSH3 c.495A>G (p.Lys165=) substitution; population rarity is assessed independently of any functional or clinical classification.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact ClinVar record is NM_002439.5(MSH3):c.495A>G (p.Lys165=), but it has three laboratory submissions classified Likely benign, all with single-submitter review status, and zero expert-panel submissions. Therefore the required expert-panel Pathogenic/Likely pathogenic assertion is absent and PP5 is not met. Ordinary laboratory submissions, aggregate labels, and the cited publications do not qualify.

Rule

PP5 supporting only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; this condition is not satisfied.

Evidence considered

• ClinVar exact-match record VCV000825321 for NM_002439.5:c.495A>G reports Likely benign and review status criteria provided by single submitter.
• The ClinVar submission audit records three exact-match laboratory submissions, zero expert-panel submissions, and no Pathogenic or Likely pathogenic expert-panel classification.
• The exact-variant papers reviewed do not provide a qualifying expert-panel assertion; their general ACMG or cancer-guideline content cannot trigger PP5.

Sources

Reasoning

No governing MSH3 VCEP or gene-specific framework was available, so the supplied generic ACMG/AMP BA1 threshold of allele frequency >=0.05 was used. The highest observed frequency is 6.27113e-05 in gnomAD v4.1 European non-Finnish individuals; the overall gnomAD v4.1 frequency is 4.77112e-05, and the gnomAD v2.1 non-cancer exome frequency is 1.68873e-05. All are far below 0.05, so BA1 is not met.

Rule

Generic BA1: allele frequency >=0.05; no applicable VCEP specification was available.

Evidence considered

• Generic ACMG/AMP BA1 stand-alone threshold: allele frequency >=0.05 (ACMG/AMP 2015, PMID:25741868).
• gnomAD v4.1 reports overall AF 4.77112e-05 and highest observed population AF 6.27113e-05 in European non-Finnish individuals, with 0 homozygotes.
• gnomAD v2.1 non-cancer exomes report AF 1.68873e-05 (4/236864 alleles) and 0 homozygotes.

Sources

Reasoning

No governing MSH3 VCEP or gene-specific framework was available, so the supplied generic BS1 threshold of allele frequency >=0.01 was used. The highest observed frequency is 6.27113e-05 in gnomAD v4.1 European non-Finnish individuals; gnomAD v4.1 overall AF is 4.77112e-05, and gnomAD v2.1 non-cancer exome AF is 1.68873e-05. These frequencies do not reach 0.01, so BS1 is not met.

Rule

Generic BS1: allele frequency >=0.01; no applicable VCEP specification was available.

Evidence considered

• Generic BS1 threshold: allele frequency >=0.01 (generic SVI default; Whiffin et al. 2017, PMID:28518168).
• gnomAD v4.1 reports overall AF 4.77112e-05 and highest observed population AF 6.27113e-05 in European non-Finnish individuals, with 0 homozygotes.
• gnomAD v2.1 non-cancer exomes report AF 1.68873e-05 (4/236864 alleles) and 0 homozygotes.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The exact ClinVar record is NM_002439.5(MSH3):c.495A>G (p.Lys165=), but it has three laboratory submissions classified Likely benign, all with single-submitter review status, and zero expert-panel submissions. Therefore the required expert-panel Benign/Likely benign assertion is absent and BP6 is not met. Ordinary laboratory submissions and aggregate ClinVar labels do not qualify.

Rule

BP6 supporting only for an exact-variant ClinVar expert-panel Benign or Likely benign classification; this condition is not satisfied.

Evidence considered

• ClinVar exact-match record VCV000825321 for NM_002439.5:c.495A>G reports Likely benign with laboratory single-submitter assertions.
• The ClinVar submission audit records three exact-match submissions, zero expert-panel submissions, and no expert-panel Benign or Likely benign classification.
• The cited publications and ordinary laboratory submissions cannot trigger BP6 under the required expert-panel-only rule.

Sources

Reasoning

No case-level evidence documents a de novo occurrence of MSH3 NM_002439.5:c.495A>G, including a confirmed proband genotype, parental genotypes, or maternity and paternity confirmation. The available materials contain no family-based testing or phenotype-linked de novo observation from which PS2 can be assessed.

Evidence considered

• The case materials provide no proband-parent trio results, parental testing, or other validated de novo documentation for NM_002439.5:c.495A>G.
• The extracted literature contains no report of this exact MSH3 variant or a relevant de novo observation.

Still missing

• Proband and parental variant-testing results are unavailable.
• Maternity and paternity confirmation are unavailable.
• A phenotype-consistent de novo case observation is unavailable.

Reasoning

The variant is synonymous, NM_002439.5:c.495A>G (NP_002430.3:p.(Lys165=)), and the available case evidence contains no validated experimental assay measuring MSH3 function, RNA processing, or mismatch-repair activity for this exact variant. SpliceAI reports a maximum delta score of 0.003, but this is computational prediction rather than functional assay evidence and cannot establish PS3. Therefore PS3 cannot be assessed from the available evidence.

Evidence considered

• The variant is synonymous: NM_002439.5:c.495A>G produces NP_002430.3:p.(Lys165=).
• No exact-variant functional assay, RNA assay, protein assay, or mismatch-repair assay is reported in the available case evidence.
• SpliceAI predicts a maximum delta score of 0.003; this computational result does not qualify as PS3 functional evidence.

Still missing

• A validated assay directly evaluating MSH3 function, RNA processing, or mismatch-repair activity for NM_002439.5:c.495A>G is needed to assess PS3.

Sources

Reasoning

No applicable MSH3 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP definition applies. The available evidence contains no case-control comparison, affected-case count for this exact variant, odds ratio, likelihood ratio, or statistically significant enrichment against controls. The exact-variant papers reviewed do not report MSH3 c.495A>G or p.Lys165= clinical cases. Therefore PS4 cannot be assessed; absence of an enrichment dataset is not evidence against enrichment.

Rule

Generic PS4: statistically significant enrichment of the variant in affected individuals compared with controls; no numeric result was available.

Evidence considered

• No MSH3 VCEP or gene-specific framework was retrieved; generic ACMG/AMP criteria were therefore used.
• The exact-variant literature extracts for PMID:25394175 and PMID:33516529 report that MSH3 c.495A>G and p.Lys165= were not mentioned and provide no variant-specific clinical data.
• No case-control enrichment metric or odds ratio for NM_002439.5:c.495A>G was present in the reviewed case evidence.

Still missing

• Exact-variant affected-case and control counts from a defined cohort
• A case-control enrichment statistic with its study design and confidence interval

Sources

Reasoning

No applicable MSH3-specific VCEP or gene framework was available, so generic ACMG/AMP PM3 was considered. PM3 requires an affected individual with the variant established in trans with a pathogenic or likely pathogenic allele, with strength based on the number and quality of such observations. The available evidence contains no affected-proband genotype, phase result, second pathogenic MSH3 allele, biallelic observation, or segregation information for NM_002439.5:c.495A>G; therefore PM3 cannot be assessed.

Rule

Generic ACMG/AMP PM3: apply only when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual; increase strength only for adequately documented independent observations.

Evidence considered

• No MSH3-specific VCEP or gene-specific allelic rule was identified; generic ACMG/AMP PM3 was therefore the applicable fallback.
• The available case evidence does not provide affected-proband genotypes, a pathogenic second MSH3 allele, trans phase, biallelic observations, or segregation data for NM_002439.5:c.495A>G.

Still missing

• Affected-proband observations with clinical phenotype are unavailable.
• A second pathogenic or likely pathogenic MSH3 variant and its trans phase are unavailable.
• Family segregation or other validated allelic evidence is unavailable.

Reasoning

No case-level evidence documents an assumed de novo occurrence of MSH3 NM_002439.5:c.495A>G without confirmed parental testing. There is no reported proband phenotype, family history, parental genotype information, or other clinically interpretable basis for applying PM6.

Evidence considered

• The case materials contain no assumed-de-novo clinical observation for NM_002439.5:c.495A>G.
• The extracted literature contains no exact-variant clinical report relevant to PM6.

Still missing

• A clinically described proband with the variant is unavailable.
• Parental testing or a documented basis for assuming de novo status is unavailable.
• Phenotype consistency and family history are unavailable.

Reasoning

No affected relatives carrying MSH3 NM_002439.5:c.495A>G, informative meioses, or phenotype-consistent family segregation data are reported. Consequently, there is no segregation count or family structure from which PP1 strength can be assigned.

Evidence considered

• No family segregation study or affected-relative genotype data are present for NM_002439.5:c.495A>G.
• The extracted literature provides no exact-variant segregation findings.

Still missing

• Family pedigree and affected-relative genotypes are unavailable.
• The number of informative meioses is unavailable.
• Phenotype consistency among variant-positive relatives is unavailable.

Reasoning

No applicable MSH3 VCEP or gene-specific framework was retrieved. The case materials do not provide a defined patient phenotype, a highly specific phenotype-disease match, or evidence that the phenotype is characteristic of an MSH3-related disorder for this exact variant. General mismatch-repair or cancer references are not sufficient to establish PP4.

Rule

Generic PP4: the patient's phenotype or family history is highly specific for a disease with a single-gene etiology; no qualifying phenotype was documented.

Evidence considered

• The reviewed case materials do not document a specific phenotype for a patient carrying NM_002439.5:c.495A>G.
• General endometrial-cancer and mismatch-repair guidance in PMID:25394175 and PMID:33516529 is not variant-specific and does not establish a highly specific MSH3 phenotype.

Still missing

• A documented patient phenotype and diagnostic context
• Evidence that the phenotype is highly specific for an MSH3-related disorder

Sources

Reasoning

The available population datasets show no homozygotes: gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer exomes, and gnomAD v3.1 non-cancer genomes each report 0 homozygotes. Although heterozygous observations are present, the available data do not establish that identified carriers are healthy adults or otherwise provide the phenotype and penetrance information required to apply BS2. BS2 therefore cannot be assessed from this evidence alone.

Rule

BS2 requires observation in healthy adults or equivalent unaffected individuals; population allele presence without carrier phenotype or penetrance data is insufficient.

Evidence considered

• gnomAD v2.1 reports 0 homozygotes among 7 observed alleles, and gnomAD v4.1 reports 0 homozygotes among 77 observed alleles.
• The gnomAD v2.1 non-cancer exome subset reports 0 homozygotes among 4 alleles; the gnomAD v3.1 non-cancer genome subset reports 0 homozygotes among 2 alleles.
• BS2 requires appropriately healthy individuals and cannot be inferred solely from an unphenotyped population database.

Still missing

• No documented phenotype, age, health status, or penetrance information is available for the observed heterozygous carriers.
• No gene-specific BS2 specification is available for MSH3.

Sources

Reasoning

The variant is synonymous, NM_002439.5:c.495A>G (NP_002430.3:p.(Lys165=)), but the available case evidence contains no validated experimental assay demonstrating preserved MSH3 function, normal RNA processing, or normal mismatch-repair activity for this exact variant. SpliceAI reports a maximum delta score of 0.003, but computational prediction alone cannot establish BS3. Therefore BS3 cannot be assessed from the available evidence.

Evidence considered

• The variant is synonymous: NM_002439.5:c.495A>G produces NP_002430.3:p.(Lys165=).
• No exact-variant functional assay, RNA assay, protein assay, or mismatch-repair assay is reported in the available case evidence.
• SpliceAI predicts a maximum delta score of 0.003; this computational result does not qualify as BS3 functional evidence.

Still missing

• A validated assay directly demonstrating preserved MSH3 function, normal RNA processing, or normal mismatch-repair activity for NM_002439.5:c.495A>G is needed to assess BS3.

Sources

Reasoning

No non-segregation evidence is available: the case materials do not identify unaffected relatives who were tested and found to carry MSH3 NM_002439.5:c.495A>G, nor do they document an informative pedigree in which the variant fails to track with the relevant phenotype.

Evidence considered

• The case materials contain no tested unaffected relatives or other family-based non-segregation evidence for NM_002439.5:c.495A>G.
• The extracted literature contains no exact-variant non-segregation finding.

Still missing

• Genotypes and phenotypes of tested unaffected relatives are unavailable.
• An informative pedigree demonstrating non-segregation is unavailable.
• The number and informativeness of non-segregating meioses are unavailable.

Reasoning

No applicable MSH3-specific VCEP or gene framework was available, so generic ACMG/AMP BP2 was considered. BP2 requires observation of the variant in trans with a pathogenic variant for a disorder that is not fully penetrant, or in cis with a pathogenic variant for a disorder with a dominant inheritance pattern. The available evidence contains no affected-proband or family genotype data, no phase information, and no documented pathogenic variant in cis or trans with NM_002439.5:c.495A>G; therefore BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2: apply only with documented phase showing the variant in trans with a pathogenic variant for a non-fully-penetrant disorder or in cis with a pathogenic variant for a dominant disorder.

Evidence considered

• No MSH3-specific VCEP or gene-specific allelic rule was identified; generic ACMG/AMP BP2 was therefore the applicable fallback.
• The available case evidence does not provide a pathogenic variant in cis or trans, phase information, or an affected-proband or family inheritance observation for NM_002439.5:c.495A>G.

Still missing

• A documented pathogenic variant in the same individual is unavailable.
• Cis/trans phase information is unavailable.
• An applicable affected-proband or family inheritance observation is unavailable.

Reasoning

No applicable MSH3 VCEP or gene-specific framework was retrieved. The available evidence does not identify an affected individual carrying this exact variant who has a confirmed alternative molecular explanation for the phenotype or disease. The ClinVar Likely benign laboratory submissions are not, by themselves, BP5 evidence, and no exact-variant alternate molecular diagnosis is documented.

Rule

Generic BP5: a pathogenic variant for the phenotype has been identified in an affected individual carrying the assessed variant; no qualifying case was documented.

Evidence considered

• The case evidence contains no documented exact-variant affected individual with a separate pathogenic molecular diagnosis explaining the phenotype.
• ClinVar contains only laboratory Likely benign submissions and does not document an alternative molecular explanation for an affected case.

Still missing

• An affected individual or family carrying the exact variant
• A confirmed alternative molecular diagnosis explaining that individual's phenotype

Sources

Reasoning

BP7 is applicable because NM_002439.5:c.495A>G is synonymous, p.(Lys165=). SpliceAI predicts minimal splice impact with a maximum delta score of 0.003, below the generic <=0.1 benign-support threshold, but the available evidence does not establish that the altered nucleotide is outside a conserved region, another required BP7 condition. Consequently, BP7 cannot be fully assessed without conservation or an applicable VCEP-specific BP7 determination.

Rule

generic_bp7: synonymous variant, no predicted splice impact, and not in a conserved region

Evidence considered

• The normalized consequence is synonymous: NM_002439.5:c.495A>G, NP_002430.3:p.(Lys165=).
• SpliceAI is available and reports DS_AG 0.003, DS_AL 0.000, DS_DG 0.000, and DS_DL 0.000; maximum delta score is 0.003.
• Generic BP7 requires a synonymous variant with no predicted splice impact and evidence that the altered nucleotide is not in a conserved region; the conservation component is not present in the case evidence.

Still missing

• Conservation status of the altered nucleotide is not available; BP7 requires evidence that the synonymous change is not in a conserved region.

Sources