RAD21 c.165A>G, p.(Thr55=)

Reasoning

The variant is absent or extremely rare in the available population databases: gnomAD v4.1 shows 26/1,611,624 alleles (AF 1.61328e-05; group-max FAF 1.456e-05) with no homozygotes, gnomAD v2.1 shows 1/251,066 alleles (AF 3.98302e-06) with no homozygotes, and gnomAD-Canada v1.0 reports absence. This supports PM2 at supporting strength under the generic fallback; no VCEP-specific RAD21 rule was available.

Rule

Generic ACMG/AMP PM2: the variant is absent from population databases or present at an extremely low frequency in controls; apply at supporting strength when the disease mechanism and available population data are compatible.

Evidence considered

• gnomAD v4.1: 26/1,611,624 alleles, AF 1.61328e-05, group-max FAF 1.456e-05, 0 homozygotes.
• gnomAD v2.1: 1/251,066 alleles, AF 3.98302e-06, 0 homozygotes.
• gnomAD-Canada v1.0: absent.
• The variant is a synonymous RAD21 c.165A>G (p.Thr55=) substitution; no population observation indicates a common polymorphism or homozygous tolerance signal.

Sources

Reasoning

SpliceAI predicts no significant splice impact for NM_006265.2:c.165A>G (max delta score = 0.003; DS_AG=0.001, DS_AL=0.002, DS_DG=0.003, DS_DL=0.0), well below the ~0.2 threshold typically used to flag a potential splice effect. No CSPEC/VCEP specification for RAD21 was found, so the generic ACMG/AMP multiple-lines-of-computational-evidence approach applies to the splice-impact path. This is the only calibrated computational prediction available for this variant (REVEL and BayesDel scores are not applicable/not found), and it is concordant with a benign impact, supporting BP4 at supporting strength.

Rule

generic_acmg_fallback

Evidence considered

• SpliceAI max delta score = 0.003 across all four splice-altering categories (acceptor gain/loss, donor gain/loss), indicating no predicted splicing disruption.

Still missing

• No gene-specific RAD21 PP3/BP4 lookup table was available; generic SpliceAI-threshold reasoning was used instead of a VCEP-calibrated rule.

Sources

Reasoning

NM_006265.2:c.165A>G is a synonymous variant (NP_006256.1:p.(Thr55=)) that does not disrupt the reference splice consensus sequence and has no predicted splicing impact by SpliceAI (max delta score = 0.003, all four scores <0.01). No CSPEC/VCEP specification for RAD21 was found (framework_mode=generic_acmg), so generic ACMG/AMP BP7 criteria apply: a synonymous variant for which splicing prediction algorithms predict no impact on the splice consensus sequence and the nucleotide is not highly conserved qualifies for BP7. No nucleotide-conservation data (e.g., GERP/PhyloP) was present in the evidence bundle to further corroborate lack of conservation, but the absence of predicted splice impact alone satisfies the core BP7 requirement under generic ACMG/AMP.

Rule

generic_acmg_fallback

Evidence considered

• Variant is synonymous, NP_006256.1:p.(Thr55=), per normalization data in case_summary.json.
• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.003).

Still missing

• No nucleotide conservation score (e.g., GERP++, PhyloP) was available in the evidence bundle to independently corroborate lack of conservation at this position.

Sources

Reasoning

NM_006265.2:c.165A>G is a synonymous variant (NP_006256.1:p.(Thr55=)). No ClinGen VCEP CSPEC was found for RAD21 (framework_mode=generic_acmg, cspec.found=false), and no gene-specific PP3/BP4 lookup spreadsheet was located in vcep_materials. Applying generic ACMG/AMP: the only computational predictor with data is SpliceAI, which shows a max delta score of 0.003 (DS_AG=0.001, DS_AL=0.002, DS_DG=0.003, DS_DL=0.0), far below the ~0.2 threshold used to flag splice-altering variants, so there is no computational evidence of deleterious effect to support PP3. REVEL and BayesDel are not applicable as this is a synonymous change with no missense consequence, and REVEL/BayesDel scores were not found in prefetch regardless (revel.found=false, bayesdel.found=false).

Rule

generic_acmg_fallback

Evidence considered

• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.003), well below the ~0.2 deleterious threshold commonly used in ClinGen SVI-aligned frameworks.

Still missing

• No gene-specific RAD21 PP3/BP4 lookup table was available to check for a pre-assigned splice-impact code.
• No CSPEC/VCEP framework found for RAD21; generic ACMG fallback used.

Sources

Reasoning

The variant is far below the generic population-frequency threshold for BA1. gnomAD v4.1 reports 26/1,611,624 alleles (AF 1.61328e-05; 0 homozygotes), with the highest population AF 2.12185e-05 in non-Finnish Europeans; gnomAD v2.1 reports 1/251,066 alleles (AF 3.98302e-06; 0 homozygotes). These frequencies do not support a stand-alone benign frequency finding.

Rule

Generic ACMG/AMP BA1: apply only when the allele frequency is greater than 5% in a population database; this variant does not approach that threshold.

Evidence considered

• gnomAD v4.1: 26/1,611,624 total alleles, AF 1.61328e-05, 0 homozygotes; highest observed population AF 2.12185e-05 in European (non-Finnish) individuals.
• gnomAD v2.1: 1/251,066 total alleles, AF 3.98302e-06, 0 homozygotes; highest observed subpopulation AF 0.000163292 in Remaining individuals.
• The observed frequency is orders of magnitude below the generic BA1 threshold of 5%; no threshold artifact or ancestry-specific elevation reaches BA1.

Sources

Reasoning

No case-level documentation of a de novo occurrence is present. The bundle does not provide proband genotype confirmation together with confirmed maternity and paternity, parental genotypes, or a de novo observation for NM_006265.2:c.165A>G.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in a patient with the disease and no family history, with maternity and paternity confirmed; apply only when case-level parental testing supports de novo status.

Evidence considered

• The consolidated case-evidence bundle contains no proband/parental testing results, de novo designation, pedigree, or meiosis information for this variant.

Still missing

• Proband and both parental genotypes for NM_006265.2:c.165A>G
• Confirmed maternity and paternity
• Case-level documentation that the variant is absent in both biological parents

Reasoning

No RAD21 ClinGen VCEP specification exists for this gene (cspec.found=false; generic ACMG framework applies). The variant NM_006265.2:c.165A>G is a synonymous change (NP_006256.1:p.(Thr55=)). No functional/splicing assay data (e.g., minigene, RT-PCR, RNA-seq, in vitro cohesin-loading or biochemical activity assay) for this variant appears anywhere in the case bundle (source_registry, prefetch, evidence, literature_pass, vcep_materials, fulltext_map). The only literature retrieved are a GeneReviews overview (PMID:20301283) and a general Sherloc methodology paper (PMID:28492532); neither reports variant-specific functional or splicing assay results.

Still missing

• No published functional/splicing assay (minigene, RT-PCR, patient RNA, or biochemical/cohesin-loading study) identified for this exact variant.
• SpliceAI prediction data is available in source_registry but was not surfaced with a computed score in the evidence bundle for this criterion pass; even if present, in silico splice prediction alone does not meet PS3 (requires validated functional assay per ACMG/AMP).

Reasoning

No case-control enrichment analysis, affected-case count, or statistically interpretable disease-cohort comparison for the exact variant NM_006265.2:c.165A>G was provided. The literature packet contains only a ClinVar-linked candidate PMID without extracted case-level evidence or an auditable full-text finding, so PS4 cannot be applied.

Rule

Generic ACMG/AMP PS4 requires statistically significant increased prevalence of the exact variant in affected individuals compared with appropriate controls; no such data are available.

Evidence considered

• The case bundle reports no CSPEC/VCEP or gene-specific framework for RAD21 and therefore uses generic ACMG/AMP fallback.
• The literature packet lists PMID:20301283 as a PS4 candidate, but provides no abstract snippet, case count, control comparison, exact-variant finding, direct quote, or location; this is insufficient to apply PS4.
• The exact ClinVar record is a single non-expert laboratory submission and does not constitute case-control enrichment evidence.

Still missing

• Exact-variant case series or case-control data with affected and control counts and an interpretable enrichment estimate are unavailable.
• No auditable publication-level case evidence was available for this exact synonymous variant.

Reasoning

No applicable RAD21 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP framework was used. The case bundle contains no affected-proband observations, second pathogenic or likely pathogenic allele, parental testing, phase information, or other evidence demonstrating the candidate variant in trans with a pathogenic variant. PM3 therefore cannot be applied.

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, with strength determined by the quality and number of observations; no such observation is documented here.

Evidence considered

• The case bundle identifies the variant as NM_006265.2:c.165A>G (p.Thr55=) in RAD21 and reports no phase, affected-proband, compound-heterozygous, or parental-inheritance observations.
• The case bundle states that no CSPEC/VCEP or local gene-specific framework was found; generic ACMG/AMP fallback was therefore used.

Still missing

• No documented second pathogenic or likely pathogenic RAD21 variant in an affected proband.
• No parental testing or phasing establishing trans configuration.
• No inheritance-mode-specific evidence permitting PM3 assessment.

Reasoning

No case-level documentation supports a presumed de novo occurrence. Neither parental testing nor a clinical report establishing de novo status without confirmed maternity and paternity is available in the bundle.

Rule

Generic ACMG/AMP PM6: presumed de novo occurrence in a patient with the disease and no family history when maternity and paternity are not confirmed; apply only with adequate case-level documentation.

Evidence considered

• The consolidated case-evidence bundle contains no parental results, pedigree, family-history statement, or presumed-de novo documentation for NM_006265.2:c.165A>G.

Still missing

• A clinical case report or laboratory record describing presumed de novo occurrence
• Parental genotype information, even if maternity and paternity are not molecularly confirmed
• Phenotype and family-history details for the relevant proband

Reasoning

No informative affected or unaffected relatives, pedigree, co-segregation observations, or meioses are documented for this variant. Therefore, segregation evidence cannot be evaluated or assigned any strength.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength depends on the number and informativeness of meioses and phenotype consistency.

Evidence considered

• The consolidated case-evidence bundle contains no family segregation data, relative testing, pedigree, or meiosis count for NM_006265.2:c.165A>G.

Still missing

• Pedigree identifying informative relatives
• Variant genotypes and phenotype status for relatives
• Number of informative meioses and segregation results
• Phenotype consistency among variant-positive relatives

Reasoning

The bundle does not provide a patient phenotype or a sufficiently specific clinical description for the exact variant. Although the ClinVar condition label is Cornelia de Lange syndrome 4, that non-expert aggregate record is not a patient-level phenotype assessment and cannot establish a highly specific phenotype-genotype match.

Rule

Generic ACMG/AMP PP4 requires a phenotype or highly specific phenotype pattern consistent with a disease for which the gene has a well-established etiology; no patient-level phenotype evidence is available.

Evidence considered

• The case bundle identifies RAD21 and the synonymous variant NM_006265.2:c.165A>G (p.Thr55=), but contains no patient phenotype summary supporting PP4.
• The ClinVar condition label is Cornelia de Lange syndrome 4, but the record is a single-submitter, non-expert assertion and is not sufficient to infer PP4.

Still missing

• Patient-level phenotype and clinical diagnostic details are absent.
• A well-established, highly specific phenotype for RAD21-related disease cannot be matched to this patient from the supplied evidence.

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact ClinVar record has one criteria-provided single-submitter laboratory assertion of Likely benign and zero expert-panel submissions, so PP5 cannot be applied.

Rule

Apply PP5 only when the exact variant has a ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• The exact ClinVar variation record is NM_006265.3(RAD21):c.165A>G (p.Thr55=), classified Likely benign with review status criteria provided, single submitter.
• ClinVar submission audit reports one submission, zero expert-panel submissions, and the submitter as Labcorp Genetics (formerly Invitae), Labcorp; this does not meet the required expert-panel criterion lead.
• The ClinVar classification is not used as PP5 because it is neither an expert-panel Pathogenic nor Likely pathogenic assertion.

Still missing

• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is present.

Sources

Reasoning

The available population data show an extremely low allele frequency, not an allele frequency greater than expected for a RAD21-related disorder. However, no RAD21-specific disease prevalence, penetrance, inheritance-based maximum credible allele frequency, or VCEP threshold was retrieved. Therefore BS1 cannot be formally assessed against a disorder-specific expected-frequency threshold.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; apply only with an appropriate disease-specific expected-frequency or maximum credible allele-frequency threshold.

Evidence considered

• gnomAD v4.1 reports AF 1.61328e-05 overall, group-max FAF 1.456e-05, and highest population AF 2.12185e-05 in non-Finnish Europeans.
• gnomAD v2.1 reports AF 3.98302e-06 overall and highest subpopulation AF 0.000163292 in Remaining individuals.
• gnomAD-Canada v1.0 reports the variant as absent.
• These observations are not compatible with a generic interpretation of increased frequency, but frequency alone cannot establish BS1 without a disorder-specific expected-frequency threshold.

Still missing

• RAD21-specific maximum credible allele frequency or other validated BS1 threshold.
• Disease prevalence and penetrance estimates for the relevant RAD21 phenotype to calculate an expected maximum allele frequency.

Sources

Reasoning

No healthy adult homozygotes or healthy adult individuals with a genotype that would be expected to cause the relevant RAD21 disorder are documented in the supplied evidence. gnomAD v2.1 and v4.1 both report zero homozygotes, but absence of homozygotes is not itself a formal BS2 observation and does not establish the required healthy-adult genotype/phenotype evidence.

Rule

Generic ACMG/AMP BS2: the variant is observed in a healthy adult individual for a disorder with full penetrance expected at an early age, or in healthy adults homozygous for a recessive disorder; population absence of homozygotes is not BS2 evidence.

Evidence considered

• gnomAD v4.1 reports 0 homozygotes among 1,611,624 alleles.
• gnomAD v2.1 reports 0 homozygotes among 251,066 alleles.
• gnomAD-Canada v1.0 reports the variant as absent and provides no homozygote or phenotype observation.
• No source in the case bundle documents healthy adult homozygotes, healthy adults with a clearly disease-inconsistent genotype, or phenotype/penetrance data sufficient for BS2.

Still missing

• A well-characterized healthy-adult cohort documenting homozygotes or otherwise disease-inconsistent genotypes for this RAD21 variant.
• Phenotype, age, ascertainment, and penetrance information for any healthy carriers used for BS2.

Sources

Reasoning

No RAD21 ClinGen VCEP specification exists for this gene (cspec.found=false; generic ACMG framework applies). No functional or splicing assay data demonstrating a lack of damaging effect (well-validated in vitro/in vivo assay showing no impact on protein function or splicing) is present anywhere in the case bundle for NM_006265.2:c.165A>G. The retrieved literature (PMID:20301283 GeneReviews overview; PMID:28492532 Sherloc methodology) contains no variant-specific functional assay results.

Still missing

• No published functional or splicing assay for this exact variant was identified to support a benign functional effect.

Reasoning

No unaffected relatives known to carry the variant, non-segregation analysis, or informative family data are reported. The absence of segregation evidence is not itself evidence for BS4.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; apply only when informative affected relatives are shown not to carry the variant and phenocopies/age-related penetrance have been considered.

Evidence considered

• The consolidated case-evidence bundle contains no unaffected variant-positive relatives or other family-level non-segregation evidence for NM_006265.2:c.165A>G.

Still missing

• Unaffected relatives tested for the variant
• Reliable phenotype assessment and age-related penetrance information
• Pedigree and number of informative non-segregating meioses

Reasoning

No applicable RAD21 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP framework was used. The case bundle contains no evidence that NM_006265.2:c.165A>G occurs in cis or trans with a pathogenic or likely pathogenic variant in an affected or unaffected individual. BP2 cannot be assessed from the available evidence.

Rule

Generic ACMG/AMP BP2: apply only when the variant is observed in cis or trans with a pathogenic or likely pathogenic variant in an affected or unaffected individual, as appropriate to the disease model; no qualifying observation is documented here.

Evidence considered

• The case bundle reports only the candidate RAD21 synonymous variant and provides no allelic observations, phase data, parental testing, or second-variant information relevant to BP2.
• The case bundle states that no CSPEC/VCEP or local gene-specific framework was found; generic ACMG/AMP fallback was therefore used.

Still missing

• No documented additional pathogenic or likely pathogenic variant in the same individual.
• No phase information establishing cis or trans configuration.
• No affected-status or inheritance information for any individual carrying multiple variants.

Reasoning

No confirmed alternate molecular basis for the reported phenotype is provided. The bundle contains no patient-level phenotype, confirmed pathogenic variant in another gene, or disease mechanism demonstrating that the phenotype is better explained by an alternative molecular diagnosis.

Rule

Generic ACMG/AMP BP5 requires a pathogenic variant in an alternative gene that explains the phenotype; no such evidence is available.

Evidence considered

• The case bundle contains no alternate-gene pathogenic finding and no patient-level diagnostic information relevant to BP5.
• The generic ACMG/AMP fallback is applicable because no RAD21-specific VCEP framework was retrieved, but its use does not create alternate molecular-basis evidence.

Still missing

• Patient phenotype and diagnostic workup are unavailable.
• No confirmed pathogenic alternate-gene finding is available to support an alternate molecular basis.

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. Although the exact variant has a Likely benign single-submitter laboratory assertion, the audit documents zero expert-panel submissions; therefore BP6 cannot be applied.

Rule

Apply BP6 only when the exact variant has a ClinVar expert-panel classification of Benign or Likely benign; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• The exact ClinVar record is classified Likely benign with review status criteria provided, single submitter.
• ClinVar submission audit reports zero expert-panel submissions and one non-expert clinical laboratory submission, so the benign assertion does not qualify for BP6.
• The single-submitter Likely benign classification is deliberately not treated as BP6 under the requested expert-panel-only rule.

Still missing

• No exact-variant ClinVar expert-panel Benign or Likely benign classification is present.

Sources