NF1 c.2573C>G, p.(Ser858Cys)

Reasoning

PM2 is met at supporting strength. The variant is extremely rare in population databases: AF 1.42693e-05 (0.00143%) in gnomAD v4.1, with 23/1,611,856 alleles and zero homozygotes; AF 2.3921e-05 (0.00239%) in gnomAD v2.1, with 6/250,826 alleles and zero homozygotes. It is absent from gnomAD-Canada v1.0. These frequencies are below the <0.1% operating threshold for PM2 supporting used in this review.

Rule

Generic ACMG/AMP PM2: absent or extremely rare in population databases; supporting strength is assigned here for AF <0.1% because no applicable NF1 criterion-level specification was retrieved.

Evidence considered

• The NF1 ClinGen/CSPEC record was checked first, but no criterion-level PM2 rule was retrieved; generic ACMG/AMP PM2 guidance was applied.
• gnomAD v4.1 reports AF 1.42693e-05 (0.00143%), 23/1,611,856 alleles, and zero homozygotes; the highest listed subgroup AF is 1.94942e-05 (0.00195%).
• gnomAD v2.1 reports AF 2.3921e-05 (0.00239%), 6/250,826 alleles, and zero homozygotes.
• The variant is absent from gnomAD-Canada v1.0.
• The generic operating threshold for PM2 supporting is AF less than 0.1%; the observed frequencies satisfy this threshold.

Still missing

• Population databases do not establish disease status or penetrance for individual carriers.
• The variant is rare rather than completely absent from all population datasets.

Sources

Reasoning

BP4 is met at supporting strength. In the absence of an NF1-specific PP3/BP4 rule, the calibrated generic missense path applies: REVEL 0.042 is at or below the ClinGen SVI benign-supporting threshold. The independent splice-impact prediction is also non-disruptive (SpliceAI max delta 0.00).

Rule

Generic calibrated computational evidence: apply BP4_supporting for a missense variant with REVEL <=0.15 under the ClinGen SVI calibration (PMID:36413997); SpliceAI shows no predicted splice impact. The same computational evidence is not also used for PP3.

Evidence considered

• The available NF1 CSPEC framework is incomplete and contains no PP3/BP4-specific rule payload, gene-specific computational lookup, or pre-assigned criterion for this variant.
• REVEL score is 0.042. The ClinGen SVI calibrated REVEL thresholds published in PMID:36413997 use REVEL >=0.70 for PP3 and <=0.15 for BP4; 0.042 meets the BP4 threshold.
• SpliceAI Lookup reports a maximum delta score of 0.00 and predicts no significant splice impact for NM_001042492.3:c.2573C>G.
• BayesDel score -0.546775 was not used because no verified published BayesDel threshold is available in this evidence bundle.

Sources

Reasoning

PP3 is not met. The NF1 CSPEC record supplied no PP3/BP4-specific rule or pre-assigned lookup result, so the generic calibrated computational-evidence framework was used. REVEL is 0.042, below the pathogenic-supporting threshold; SpliceAI max delta is 0.00 and predicts no splice impact.

Rule

Generic calibrated computational evidence: do not apply PP3 when REVEL is below the ClinGen SVI pathogenic-supporting threshold; the concurrent SpliceAI prediction is non-disruptive.

Evidence considered

• The available NF1 CSPEC framework is incomplete and contains no PP3/BP4-specific rule payload, gene-specific computational lookup, or pre-assigned criterion for this variant.
• REVEL score is 0.042. The ClinGen SVI calibrated REVEL thresholds published in PMID:36413997 use REVEL >=0.70 for PP3 and <=0.15 for BP4; this score does not support PP3.
• SpliceAI Lookup reports a maximum delta score of 0.00 and predicts no significant splice impact for NM_001042492.3:c.2573C>G.

Sources

Reasoning

No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification exists for c.2573C>G (p.Ser858Cys); PP5 is not met.

Rule

Apply PP5 only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• The exact ClinVar record has nine submissions and zero expert-panel submissions. Its listed assertions are six uncertain significance, two likely benign, and one benign, all from single submitters.

Sources

Reasoning

BA1 is not met. The highest observed population frequency is 0.00143% in gnomAD v4.1 overall and 0.00195% in the European (non-Finnish) subgroup, far below the generic 1% benign stand-alone threshold. gnomAD v2.1 is also far below this threshold.

Rule

Generic ACMG/AMP BA1: population allele frequency is sufficiently high for a benign stand-alone assertion; operating threshold used here is >1% because no applicable NF1 criterion-level specification was retrieved.

Evidence considered

• The NF1 ClinGen/CSPEC record was checked first, but no criterion-level rules were retrieved; generic ACMG/AMP population thresholds were therefore used.
• gnomAD v4.1 reports 23/1,611,856 alleles, AF 1.42693e-05 (0.00143%), with the highest reported subgroup AF 1.94942e-05 (0.00195%) in European (non-Finnish) individuals.
• gnomAD v2.1 reports 6/250,826 alleles, AF 2.3921e-05 (0.00239%), with the highest reported subgroup AF 5.29811e-05 (0.00530%) in European (non-Finnish) individuals.
• The generic operating threshold for BA1 is AF greater than 1%; the observed frequencies do not approach this threshold.

Sources

Reasoning

BS1 is not met. The observed allele frequencies are substantially below the generic disease-prevalence-based benign-frequency threshold used for this review (>0.3%), including the highest observed subgroup frequency of 0.00195% in gnomAD v4.1.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; operating threshold used here is >0.3% because no applicable NF1 criterion-level specification was retrieved.

Evidence considered

• The NF1 ClinGen/CSPEC record was checked first, but it contains no retrieved criterion-level BS1 rule; generic ACMG/AMP population thresholds were used.
• gnomAD v4.1 reports overall AF 1.42693e-05 (0.00143%) and maximum listed subgroup AF 1.94942e-05 (0.00195%).
• gnomAD v2.1 reports overall AF 2.3921e-05 (0.00239%) and maximum listed subgroup AF 5.29811e-05 (0.00530%).
• The generic operating threshold for BS1 is AF greater than 0.3%; neither the overall nor subgroup frequencies meet it.

Sources

Reasoning

No exact-variant ClinVar expert-panel Benign or Likely benign classification exists for c.2573C>G (p.Ser858Cys); BP6 is not met.

Rule

Apply BP6 only to an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• The exact ClinVar record has nine submissions and zero expert-panel submissions. The benign and likely benign assertions are single-submitter laboratory assertions and cannot trigger BP6.

Sources

Reasoning

The variant is NF1 p.Ser858Cys, but the case bundle contains no validated same-amino-acid substitution at this residue with established pathogenic or likely pathogenic evidence. ClinVar records for the submitted variant are not usable as same-amino-acid comparator evidence, and no relevant paper extraction reports such a comparator.

Evidence considered

• The case variant is NM_001042492.3:c.2573C>G, NP_001035957.1:p.(Ser858Cys).
• The available paper extractions contain no variant-specific or same-amino-acid comparator evidence for residue 858.

Still missing

• A validated pathogenic or likely pathogenic NF1 variant producing p.Ser858Cys from a different nucleotide change is not documented in the available evidence bundle.

Reasoning

No proband-level de novo observation is documented in the case-evidence bundle. There is no parental testing result establishing that the NF1 c.2573C>G (p.Ser858Cys) variant is absent from both biological parents, and no information on maternity/paternity, mosaicism assessment, or technical confirmation is provided.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no confirmed family history, with stronger application requiring appropriately documented parental testing and phenotype consistency; no qualifying case evidence is available.

Evidence considered

• The NF1 ClinGen specification was found, but its parsed criterion payload is empty and it provides no usable PS2-specific rule in this case bundle.
• The case bundle contains no parental testing results or validated de novo observation for NM_001042492.3:c.2573C>G.
• ClinVar submissions and classifications were not used as evidence for PS2 because they do not document a validated de novo event in this case.

Still missing

• Documented proband phenotype and indication for testing
• Validated parental genotypes for both biological parents
• Confirmation that maternity and paternity are established
• Assessment for parental mosaicism and assay limitations

Sources

Reasoning

No variant-specific validated functional assay demonstrating a deleterious effect was identified. The applicable NF1 ClinGen specification is present but unstructured and contains no PS3 rule payload or functional-evidence calibration. The available literature extracts do not report NM_001042492.3:c.2573C>G (p.Ser858Cys), and OncoKB explicitly reports no variant-specific reviewed functional evidence.

Evidence considered

• The NF1 ClinGen specification (Version 1.0, document 1553923915) was checked first; it is marked incomplete/unstructured, with no PS3-specific rule payload or assay calibration available.
• OncoKB states that it did not identify variant-specific reviewed functional evidence for NF1 p.S858C and labels the variant-specific effect unknown.
• PMID:25741868 was reviewed for functional-evidence guidance but does not mention NF1 c.2573C>G or p.Ser858Cys and provides no variant-specific assay result.
• PMID:26467025 was reviewed for functional-evidence context but does not mention NF1 c.2573C>G or p.Ser858Cys and provides no variant-specific assay result.

Still missing

• A validated assay of NF1 p.Ser858Cys function is needed, including appropriate wild-type and known-loss-of-function controls.
• Assay relevance to NF1 biology and quantitative result thresholds for PS3 strength are unavailable.
• The NF1 VCEP framework record does not provide a usable PS3-specific calibration rule.

Sources

Reasoning

No variant-specific case-control or cohort enrichment data were retrieved for NF1 c.2573C>G (p.Ser858Cys); PS4 cannot be assessed.

Rule

Generic ACMG/AMP PS4: require a statistically significant increase in variant prevalence in affected individuals versus controls.

Evidence considered

• The retrieved NF1 CSPEC record is incomplete and contains no criterion-specific PS4 rule payload; generic ACMG/AMP PS4 assessment therefore applies.
• The literature packet's PS4 candidates were policy/guidance papers, and the precomputed extracts show no report of c.2573C>G or p.Ser858Cys.

Still missing

• Variant-specific, phenotype-defined case and control counts or a validated enrichment analysis are needed.

Sources

Reasoning

The governing NF1 ClinGen specification is identified, but its extracted ruleset is incomplete and vcep_materials.json has no NF1 domain_tables entry. Therefore, the authoritative complete domain list required for the residue-wide PM1 check is unavailable; no PM1 assertion is made from re-derived or general domain information.

Evidence considered

• The case identifies the ClinGen Neurofibromatosis and Schwannomatosis Expert Panel NF1 specification, Version 1.0, but reports framework_complete=false and rule_payload={}.
• vcep_materials.json reports domain_tables={} for NF1, so no authoritative domain entry can be checked against residue 858.

Still missing

• The governing NF1 VCEP-approved critical functional domain table or complete PM1 rule is not available in the case materials.

Sources

Reasoning

No validated pathogenic or likely pathogenic missense comparator at NF1 residue 858 is documented in the available case evidence. The PM5 candidate artifact explicitly reports zero collected same-residue candidates and advises that PM5 not be applied from that artifact alone.

Evidence considered

• The case's PM5 candidate summary reports same_residue_candidates=0 and states that classic same-residue PM5 semantics could not be confirmed safely.
• No relevant paper extraction documents an alternate missense change at NF1 residue 858.

Still missing

• A validated pathogenic or likely pathogenic NF1 missense variant at residue 858, with sufficient evidence independent of the submitted variant, is not available.

Sources

Reasoning

No presumed de novo occurrence is documented for this variant. The case-evidence bundle does not provide parental genotypes, a validated de novo report, or sufficient family and phenotype details to support PM6.

Rule

Generic ACMG/AMP PM6: presumed de novo occurrence in a patient with the disease and no confirmed family history when parental testing is unavailable or incomplete; no qualifying case evidence is available.

Evidence considered

• The NF1 ClinGen specification was found, but its parsed criterion payload is empty and it provides no usable PM6-specific rule in this case bundle.
• No case report, family report, or validated clinical record in the bundle documents a presumed de novo NF1 c.2573C>G variant.
• The available ClinVar record contains conflicting single-submitter classifications but no validated parental or de novo evidence, so those assertions were not used for PM6.

Still missing

• A published or clinically documented presumed de novo observation
• Parental testing information or an explicit explanation for why testing was unavailable
• Proband phenotype consistency with NF1
• Evaluation of possible parental mosaicism

Sources

Reasoning

No informative affected or unaffected relatives, phase data, number of informative meioses, or segregation results are provided for NF1 c.2573C>G (p.Ser858Cys). The bundle therefore cannot establish co-segregation with an NF1-consistent phenotype or assign PP1 strength.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a well-established phenotype, with strength dependent on the amount and informativeness of segregation; no qualifying segregation data are available.

Evidence considered

• The NF1 ClinGen specification was found, but its parsed criterion payload is empty and it provides no usable PP1-specific rule in this case bundle.
• The literature extraction entries available in the bundle do not mention this variant and do not report variant-specific family segregation.
• A ClinVar submitter sentence referring to an individual with NF1 and a co-occurring NF1 truncating variant was not treated as PP1 evidence because it does not document segregation, informative meioses, or a validated publication trail.

Still missing

• Pedigree identifying informative relatives
• Genotypes for affected and unaffected relatives
• Phenotype assessments for relatives using NF1 diagnostic criteria
• Number of informative meioses and segregation calculation
• Phase and relationship confirmation

Sources

Reasoning

The available NF1 specification does not provide an extractable PP2 rule, and the bundle does not establish that missense variation is a sufficiently common pathogenic mechanism for NF1 under an applicable gene-specific or generic PP2 rule. The variant-level REVEL score is not evidence for PP2.

Evidence considered

• The identified NF1 specification is incomplete and contains no extractable PP2 rule.
• The case bundle provides no validated gene-level missense-mechanism assessment sufficient to apply PP2.

Still missing

• An applicable NF1-specific or generic PP2 rule defining the gene missense mechanism and its evidentiary threshold is not available.
• Validated gene-level evidence meeting that PP2 rule is not available in the case bundle.

Sources

Reasoning

No proband phenotype, diagnostic evaluation, or phenotype-specificity evidence was provided for this variant; PP4 cannot be assessed.

Rule

Generic ACMG/AMP PP4: the patient's phenotype or family history must be highly specific for a disease with a single genetic etiology.

Evidence considered

• The retrieved NF1 CSPEC record is incomplete and contains no criterion-specific PP4 rule payload; generic ACMG/AMP PP4 assessment therefore applies.
• ClinVar condition labels are submitter-associated labels rather than a documented phenotype for the present proband and do not establish PP4.

Still missing

• Provide the proband's phenotype and the diagnostic work-up excluding alternative causes, with assessment of specificity for NF1-related disease.

Sources

Reasoning

BS2 cannot be established from the available evidence. gnomAD reports no homozygotes, but the 23 observed heterozygous alleles in gnomAD v4.1 are not documented as healthy, phenotypically evaluated individuals, and no reliable variant-specific unaffected-carrier or homozygote observation is available. The absence of homozygotes is not positive BS2 evidence.

Rule

Generic ACMG/AMP BS2: observed in healthy individuals, including homozygotes for a recessive disorder or hemizygotes for an X-linked disorder, or multiple unaffected heterozygotes when phenotype ascertainment is adequate. Population-database presence alone is insufficient.

Evidence considered

• gnomAD v4.1 reports 23 heterozygous alleles and zero homozygotes; this population count does not establish that carriers are clinically unaffected.
• The NF1 genetic-counseling review states that a positive DNA test cannot predict the presence, age of onset, or severity of NF1 symptoms, so the available population observations cannot be treated as phenotype-ascertained healthy carriers.
• BS2 requires observation in healthy individuals, typically including homozygotes for a fully penetrant dominant disorder or hemizygotes, or a sufficient number of unaffected heterozygotes with appropriate phenotype ascertainment; those data are not available here.

Still missing

• No phenotype-ascertained healthy carriers with this exact variant were identified.
• No homozygous individuals with documented unaffected status were identified.
• A disease-specific penetrance and age-related ascertainment assessment for NF1 carriers is not available for this variant.

Sources

Reasoning

No variant-specific validated functional assay demonstrating preserved NF1 function was identified. The applicable NF1 ClinGen specification is present but unstructured and contains no BS3 rule payload or functional-evidence calibration. The available literature extracts do not report NM_001042492.3:c.2573C>G (p.Ser858Cys), and OncoKB reports no variant-specific reviewed functional evidence.

Evidence considered

• The NF1 ClinGen specification (Version 1.0, document 1553923915) was checked first; it is marked incomplete/unstructured, with no BS3-specific rule payload or assay calibration available.
• OncoKB states that it did not identify variant-specific reviewed functional evidence for NF1 p.S858C and labels the variant-specific effect unknown.
• PMID:25741868 was reviewed for functional-evidence guidance but does not mention NF1 c.2573C>G or p.Ser858Cys and provides no variant-specific assay result.
• PMID:26467025 was reviewed for functional-evidence context but does not mention NF1 c.2573C>G or p.Ser858Cys and provides no variant-specific assay result.

Still missing

• A validated assay of NF1 p.Ser858Cys function is needed, including appropriate wild-type and known-benign controls.
• Assay controls, biological relevance, reproducibility, and quantitative thresholds for BS3 strength are unavailable.
• The NF1 VCEP framework record does not provide a usable BS3-specific calibration rule.

Sources

Reasoning

No unaffected relatives carrying the variant, no pedigree-based non-segregation analysis, and no phenotype/genotype comparison among informative family members are documented. Absence of segregation cannot be concluded from the lack of family data.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected family members, when the phenotype is specific and family members are adequately evaluated; no qualifying non-segregation evidence is available.

Evidence considered

• The NF1 ClinGen specification was found, but its parsed criterion payload is empty and it provides no usable BS4-specific rule in this case bundle.
• The case-evidence bundle contains no documented non-segregation observation for NF1 c.2573C>G.
• Population frequency and conflicting ClinVar classifications were not used as BS4 evidence because BS4 requires non-segregation in informative family members, not population or submitter classification data.

Still missing

• Genotypes of clinically evaluated unaffected relatives
• Reliable NF1 phenotype assessments for those relatives
• Pedigree structure and informative meioses
• Confirmation that relatives were old enough and adequately examined to be informative

Sources

Reasoning

The available NF1 specification does not provide an extractable BP1 rule, and the evidence bundle does not establish that NF1 is a gene in which missense variation is generally not a pathogenic mechanism under an applicable specification. BP1 is therefore not asserted.

Evidence considered

• The identified NF1 specification is incomplete and contains no extractable BP1 rule.
• The case bundle does not provide sufficient gene-level evidence to conclude that NF1 missense variants are generally benign or not a disease mechanism.

Still missing

• An applicable NF1-specific or generic BP1 rule and supporting gene-level missense-mechanism evidence are not available.

Sources

Reasoning

A ClinVar submitter sentence reports NF1 c.2573C>G (p.Ser858Cys) in an individual with NF1 co-occurring with an NF1 truncating variant, but it does not establish whether the variants are in trans or cis, does not provide the individual-level phenotype and genotype record, and has no validated publication trail in the bundle. Because BP2 requires documented phase and appropriate pathogenicity context for the second variant, this observation is insufficient for adjudication.

Rule

Generic ACMG/AMP BP2: observed in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant for a recessive disorder; phase and the pathogenicity of the co-occurring variant must be documented.

Evidence considered

• A ClinVar submission contains the sentence: identified in an individual with neurofibromatosis type I, co-occurring with an NF1 truncating variant (Koczkowska 2018). The submission does not document phase, and its PubMed trail is not validated in this case bundle.
• The NF1 framework specifies autosomal dominant inheritance, for which BP2 would require a reliable observation of the assessed variant in trans with a pathogenic variant in the same individual.
• The available paper-extract entries do not contain a variant-specific report of c.2573C>G/p.Ser858Cys or an auditable phase observation.

Still missing

• Validated individual-level case report or clinical record for the co-occurring NF1 truncating variant
• Direct phase determination showing whether c.2573C>G and the truncating variant are in trans
• Validated evidence establishing the truncating variant as pathogenic
• Documented NF1 phenotype and testing methodology for the reported individual

Sources

Reasoning

No primary, variant-specific evidence documents this variant in an individual whose phenotype is fully explained by an independently pathogenic molecular diagnosis; BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5: the variant is found in a case with an alternate molecular basis for the disease.

Evidence considered

• One non-expert ClinVar submission contains an unverified statement that the variant co-occurred with an NF1 truncating variant, but the submission audit found no validated publication trail and no usable criterion lead; this is insufficient for BP5.

Still missing

• Provide primary case evidence documenting the phenotype and a confirmed alternative pathogenic molecular diagnosis sufficient to explain it.

Sources