NF1 c.6737del, p.(Pro2246GlnfsTer19)

Reasoning

NM_001042492.3:c.6737del is a single-nucleotide deletion producing a frameshift, NP_001035957.1:p.(Pro2246GlnfsTer19), that introduces a premature termination codon (PTC) 19 codons downstream of the frameshift start. No official NF1 VCEP/CSPEC PVS1 decision tree text was retrievable from the case materials (cspec found=true but rule_payload is empty and no structured PVS1 rules were extracted), so the generic ClinGen SVI PVS1 framework (PMC6185798) was applied per pvs1_variant_assessment scaffold. Germline loss-of-function is an established NF1 disease mechanism: NF1 causes autosomal dominant neurofibromatosis type 1 through haploinsufficiency, and the literature consistently reports that the majority of pathogenic NF1 variants are truncating (nonsense/frameshift) mutations causing a PTC (PMID:10712197 reports 224/278, 80.6%, of pathogenic mutations caused a PTC, including 140 frameshift mutations; PMID:10862084 states NF1 clinical features are in the majority of cases caused by haploinsufficiency due to a PTC-generating mutation and rapid decay of the mutant RNA; PMID:23913538 reports that in a French cohort, roughly one-third of pathogenic variants were small indels, most with frameshift consequences). The PTC at codon ~2264 (P2246Qfs*19) falls well upstream of the transcript's final exon-exon junction relative to the mature transcript length (~2839 residues for NP_001035957.1), so nonsense-mediated decay (NMD) is predicted rather than escape, consistent with the pvs1_variant_assessment default classification of frameshift variants as PVS1-eligible once gene-level LOF mechanism is confirmed (pvs1_gene_context: lof_mechanism_supported=true, pvs1_gene_gate=eligible). The variant transcript (NM_001042492.3) matches the transcript used for ClinVar's matched pathogenic submission and for all case normalization, so transcript relevance is not a concern. SpliceAI shows no significant splice-altering signal (max delta 0.177), so this frameshift/PTC mechanism, not an aberrant splicing mechanism, governs the PVS1 call.

Rule

PVS1_generic_frameshift_NMD_predicted

Evidence considered

• pvs1_variant_assessment.json classifies c.6737del as consequence_class=frameshift, variant_bucket=frameshift, and recommends applying the generic PVS1 framework (framework_source PMC6185798) with a suggested_default_strength of PVS1, subject to confirming transcript relevance, NMD status, and exon importance.
• pvs1_gene_context.json confirms NF1 germline loss-of-function is a supported disease mechanism (lof_mechanism_supported=true, pvs1_gene_gate=eligible), based on a targeted germline literature search, since no official CSPEC/VCEP PVS1-specific ruleset was available (cautions note: 'generic PVS1 fallback should follow PMC6185798').
• PMID:10712197 (direct quote): 'Among the 278 mutations identified, we observed 84 (30.2%) nonsense mutations and 140 (50.4%) frameshift mutations... Thus, as many as 224 (80.6%) mutations caused, directly or indirectly, a premature termination codon (PTC).' This establishes that truncating/frameshift PTC-generating variants are the predominant and accepted pathogenic mechanism class in NF1, though this paper does not mention the specific variant c.6737del.
• PMID:10862084 (direct quote): 'In the majority of cases the clinical features of NF1 are caused by haploinsufficiency due to a mutation leading to a PTC and rapid decay of the mutant RNA.' This directly supports NMD/haploinsufficiency as the operative mechanism for PTC-producing NF1 variants generally; this paper does not mention the specific variant c.6737del.
• PMID:23913538 (direct quote): 'NF1 is caused by dominant loss-of-function mutations of the tumor suppressor NF1... About one-third were small insertions and/or deletions (N = 170), most of them with frameshift consequences (N = 164).' Confirms frameshift indels are a common and accepted class of pathogenic NF1 variant; this paper does not mention the specific variant c.6737del.
• case_summary.json spliceai evidence_sentence: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.18)', supporting that the frameshift/PTC mechanism (not splicing) is the relevant PVS1 pathway for this variant, per the pvs1_variant_assessment downgrade_considerations instruction not to double-count PP3 splice evidence.
• case_summary.json normalization confirms the variant transcript/protein designation NM_001042492.3:c.6737del / NP_001035957.1:p.(Pro2246GlnfsTer19), consistent across prefetch, evidence, and ClinVar matched record, supporting transcript relevance.

Still missing

• The exact exon number harboring c.6737del and the precise nucleotide distance from the PTC to the final exon-exon junction were not independently retrieved from a RefSeq/Ensembl exon map in the case bundle; NMD prediction here is inferred from the proportion of remaining coding sequence (roughly the final 21% of a ~2839-residue protein is lost) rather than a confirmed <50bp-from-last-junction rule application.
• No NF1-specific VCEP PVS1 decision-tree text (exon-skipping rescue, exon dispensability, or hotspot-exon exceptions) was available in vcep_materials (rule_payload empty), so exon-level exceptions (e.g., alternatively spliced or non-essential exon) could not be explicitly excluded, though no evidence of such an exception was found either.
• No gnomAD population LoF constraint or exon-specific pLoF depletion data was available (variant itself is absent from gnomAD v2.1/v4.1) to corroborate that the affected exon is not a region tolerant of LoF variation.

Sources

Reasoning

PM2 is met at supporting strength. The exact NF1 variant NM_001042492.3:c.6737del, a frameshift variant, is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This is compatible with a rare variant causing an autosomal-dominant disorder; no ancestry-specific population signal or frequency artifact was identified.

Rule

Generic ACMG/AMP PM2 at supporting strength: apply when the variant is absent or extremely rare in population databases appropriate for the disease context. No applicable NF1 CSPEC PM2 rule was retrievable from the available ruleset.

Evidence considered

• The exact normalized variant was reported absent from gnomAD v2.1.
• The exact normalized variant was reported absent from gnomAD v4.1.
• The exact normalized variant was reported absent from gnomAD-Canada v1.0.
• The retrieved NF1 ClinGen CSPEC document identifies the NF1 disease context and version 1.0 framework, but its ruleset was unstructured and supplied no criterion-specific PM2 threshold; therefore generic ACMG/AMP PM2 was used.
• The case bundle identifies NF1 as an autosomal-dominant disorder and the variant as a frameshift; no population frequency, ancestry enrichment, homozygote, or penetrance artifact argues against rarity.

Still missing

• The bundle does not provide total allele-number denominators or ancestry-specific coverage metrics for the absent records.
• No independently curated NF1-specific maximum credible population-frequency threshold was retrieved in the CSPEC material.

Sources

Reasoning

The exact ClinVar record is Pathogenic but has one criteria-provided single-submitter clinical-laboratory assertion (Labcorp Genetics) and no expert-panel submission. It does not meet the required exact-variant ClinVar expert-panel condition for PP5.

Rule

Apply PP5 at supporting strength only for an exact-variant ClinVar Pathogenic or Likely pathogenic expert-panel classification; ordinary laboratory submissions and aggregate ClinVar labels do not qualify.

Evidence considered

• ClinVar Variation ID 1429404 exactly matches NM_001042492.3:c.6737del and reports zero expert-panel submissions; its only listed submission is Labcorp Genetics with review status 'criteria provided, single submitter'.

Sources

Reasoning

BA1 is not met. The exact variant NM_001042492.3:c.6737del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore no population allele frequency reaches a stand-alone benign threshold.

Rule

Generic ACMG/AMP BA1: apply only when the allele frequency is stand-alone benign for the relevant disease context. No applicable NF1 CSPEC population rule was retrieved; the NF1 CSPEC ruleset was present but unstructured and contained no criterion-specific payload.

Evidence considered

• The variant was queried at the normalized GRCh37 and GRCh38 coordinates and was reported absent from gnomAD v2.1 and gnomAD v4.1.
• The variant was also reported absent from gnomAD-Canada v1.0.
• No observed allele count or frequency is available that could meet the BA1 threshold; absence is evidence against BA1, not evidence for BA1.

Sources

Reasoning

BS1 is not met. The exact variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so there is no allele frequency greater than expected for NF1 to support BS1.

Rule

Generic ACMG/AMP BS1: apply when the allele frequency is greater than expected for the disorder. No applicable NF1 CSPEC population rule was retrieved; the available NF1 CSPEC ruleset contained no criterion-specific population instructions.

Evidence considered

• The exact normalized variant was absent from gnomAD v2.1 and gnomAD v4.1.
• The exact normalized variant was absent from gnomAD-Canada v1.0.
• Because no population frequency was observed, ancestry-specific enrichment or a disease-prevalence-based excess-frequency calculation cannot produce BS1 evidence.

Sources

Reasoning

The exact ClinVar record has no expert-panel submission and its sole laboratory submission is Pathogenic, not Benign or Likely benign. It does not meet the required exact-variant ClinVar expert-panel condition for BP6.

Rule

Apply BP6 at supporting strength only for an exact-variant ClinVar Benign or Likely benign expert-panel classification; ordinary laboratory submissions and aggregate ClinVar labels do not qualify.

Evidence considered

• ClinVar Variation ID 1429404 exactly matches NM_001042492.3:c.6737del and reports zero expert-panel submissions; the only listed assertion is a Pathogenic single-submitter clinical-laboratory record.

Sources

Reasoning

No proband-specific de novo evidence is documented in the consolidated case-evidence bundle. Parental testing results, confirmation of the variant in the proband, and parental relationships are not provided; therefore PS2 cannot be assessed.

Evidence considered

• The bundle identifies an applicable NF1 ClinGen Neurofibromatosis and Schwannomatosis specification, version 1.0, but the criterion-specific rule payload is empty.
• The case-specific sections reviewed contain no proband/parent genotype results, parental testing, or de novo observation for NM_001042492.3:c.6737del.

Still missing

• Documented parental genotypes or a validated statement that both parents tested negative for the variant
• Confirmation of the variant in the proband and confirmation of biological parentage
• Relevant phenotype and family-history details supporting a de novo interpretation

Sources

Reasoning

No validated functional assay (e.g., RAS-GAP activity assay, minigene/RNA splicing assay, protein stability/expression assay) targeting this specific variant (c.6737del, p.(Pro2246GlnfsTer19)) was found in any bundled source. The NF1 CSPEC (cspec) rule_payload for PS3/BS3 was not populated (framework_complete=false, rule_payload empty), so no gene-specific PS3/BS3 calibration is available and generic ACMG applies by default, but no assay evidence exists to apply it to. PMID:10543400 reports RNA/RT-PCR-based transcript analysis in NF1 patients generally (allelic exclusion, reduced mutant transcript expression in a subset of patients) but does not mention this variant or study it directly (variant_mentioned=false). PMID:10862084, PMID:10712197, PMID:23913538, PMID:12509763, and PMID:19573811 similarly describe NF1 mutational spectra, RAS-GAP mechanism, or NF1 inactivation in glioblastoma cell lines/tumors at a gene level, none reporting a variant-specific functional study of c.6737del. OncoKB's 'Likely Loss-of-function' biological-effect label is a curated computational/literature inference, not a reported wet-lab functional assay result for this exact variant, so it cannot substantiate PS3.

Evidence considered

• PMID:10543400 discusses general NF1 transcript-level analysis (RT-PCR, protein truncation test) across a patient cohort but does not mention or study c.6737del specifically
• PMID:10862084, PMID:10712197, PMID:23913538 describe NF1 mutational spectra and general haploinsufficiency mechanism, not variant-specific functional data
• PMID:19573811 reports NF1 inactivation via proteasomal degradation and genetic loss in glioblastoma cell lines/tumors generally, not for this specific variant
• OncoKB curated 'Likely Loss-of-function' biological effect label is an inference/curation, not a reported functional assay for this exact variant, so it does not meet PS3 evidentiary standard
• cspec final_classification_framework rule_payload is empty (framework_complete=false), so no NF1-specific PS3/BS3 assay calibration rules were available to apply

Still missing

• No variant-specific functional assay (RNA, splicing minigene, protein expression/GAP activity) identified for c.6737del/p.(Pro2246GlnfsTer19)
• NF1 CSPEC PS3/BS3 assay validation criteria (rule_payload) not available in this case bundle to check whether any hypothetical assay would meet calibration thresholds

Sources

Reasoning

No case-control study, affected-case count with a defined comparator, or statistically evaluated enrichment data for NF1 c.6737del were provided. The ClinVar record is a single laboratory submission and cannot establish case-control enrichment.

Rule

Generic ACMG/AMP PS4 requires a statistically increased prevalence of the variant in affected individuals compared with controls; no applicable NF1-specific PS4 rule was retrieved from the available CSPEC material.

Evidence considered

• The exact ClinVar record (Variation ID 1429404) contains one pathogenic clinical-laboratory submission; it provides no case-control counts or enrichment statistic.

Still missing

• Variant-specific affected-case and control counts, ascertainment criteria, and a statistical enrichment analysis are needed.

Sources

Reasoning

No de novo occurrence based on assumed or unverified parental relationships is documented. Without case-level evidence of an affected proband, negative parental testing, and the basis for assuming parentage or maternity/paternity, PM6 cannot be assessed.

Evidence considered

• The applicable NF1 specification is present in the bundle, but it does not contain an available criterion-specific PM6 rule payload.
• The consolidated case-evidence bundle contains no case-level de novo report, parental relationship evidence, or parental genotype information for this variant.

Still missing

• Case report or clinical record documenting the de novo occurrence
• Parental testing or explicit documentation that testing was unavailable/uninformative
• Evidence supporting parentage and the phenotype consistency of the proband

Sources

Reasoning

No affected relatives, informative meioses, cosegregation data, or family genotypes are documented for NM_001042492.3:c.6737del. The available literature extracts concern general NF1 variant spectra or mechanism and do not report this exact variant or segregation observations; PP1 therefore cannot be assessed.

Evidence considered

• The bundle identifies the NF1 ClinGen specification as applicable, but its criterion-specific rule payload is empty.
• The paper extracts reviewed for this group do not mention c.6737del or p.(P2246Qfs*19) and provide no family segregation or meiosis data for the queried variant.
• No case-specific family history, relative genotypes, or cosegregation observations are present in the consolidated bundle.

Still missing

• Number and identity of informative affected relatives
• Genotypes and phenotypes of relatives and segregation across informative meioses
• Phenotype consistency and assessment of potentially unaffected or age-dependent relatives
• A validated NF1-specific PP1 threshold or rule if one is to be applied

Sources

Reasoning

No proband phenotype, diagnostic features, or phenotype differential was supplied. Therefore phenotype specificity for NF1-associated neurofibromatosis type 1 cannot be evaluated for this variant.

Rule

Generic ACMG/AMP PP4 requires a phenotype or family history highly specific for a disease with a single genetic etiology; no applicable NF1-specific PP4 rule was retrieved from the available CSPEC material.

Evidence considered

• The available NF1 CSPEC material identifies neurofibromatosis type 1 as the disease context but contains no retrieved PP4-specific rule content.

Still missing

• Provide the individual's clinical phenotype, age, diagnostic assessment, and relevant alternative etiologies.

Sources

Reasoning

BS2 cannot be assessed from the case bundle. No data are provided showing the exact variant in healthy adults at an age and in a number sufficient to be inconsistent with NF1, and no homozygote or hemizygote observation is reported.

Rule

Generic ACMG/AMP BS2: apply only for observations of the variant in healthy adults at an age and in numbers inconsistent with the disease, or in unaffected homozygous/hemizygous individuals for a dominant disorder. No applicable NF1 CSPEC population rule was retrieved.

Evidence considered

• The population resources in the bundle report absence of the exact variant, but they do not provide an unaffected-carrier, homozygote, or hemizygote observation that can be evaluated under BS2.
• The ClinVar record is a single pathogenic germline submission and does not establish the presence of the variant in unaffected adults.

Still missing

• No unaffected-adult carrier observations for the exact variant were provided.
• No homozygous or hemizygous observations for the exact variant were provided.
• No age, ascertainment, penetrance, or phenotype information is available for any putative healthy carriers.

Reasoning

No functional assay data indicating normal/wild-type-like function for this variant was found in any bundled source, so BS3 (evidence of normal function) cannot be applied. As with PS3, the NF1 CSPEC PS3/BS3 rule_payload was not populated in this case bundle, and none of the reviewed papers (PMID:10543400, PMID:10862084, PMID:10712197, PMID:23913538, PMID:12509763, PMID:19573811) report a functional assay result for c.6737del/p.(Pro2246GlnfsTer19); they discuss NF1 mutational spectra and mechanism at a gene level only.

Evidence considered

• No source in the case bundle reports a functional assay showing normal/wild-type activity for c.6737del; all reviewed papers are gene-level mutational-spectrum studies without variant-specific functional testing

Still missing

• No functional assay evidence of any kind (supporting damaging or benign effect) was found for this variant

Sources

Reasoning

No phenotype/genotype data for unaffected relatives carrying or lacking the variant are documented. In the absence of informative non-segregation observations and adequate assessment of age, penetrance, and phenotype, BS4 cannot be assessed.

Evidence considered

• The applicable NF1 specification is present in the bundle, but no criterion-specific BS4 rule payload is available.
• The consolidated case-evidence bundle contains no non-segregation findings, unaffected-relative genotypes, or family phenotype assessments for this variant.

Still missing

• Genotypes and clinical phenotypes of informative unaffected relatives
• Documentation that relatives are old enough and adequately evaluated for NF1 manifestations
• Pedigree structure and number of informative meioses
• Assessment of phenocopies, reduced penetrance, and variable expressivity

Sources

Reasoning

BP2 cannot be assessed from the available case bundle. The bundle contains no affected-proband genotype data, second pathogenic or likely pathogenic variant, phase determination, parental testing, or cis/trans observation for NM_001042492.3:c.6737del (p.Pro2246GlnfsTer19). The NF1 framework record is present but contains no structured BP2 rule payload.

Rule

Assess BP2 only when a second pathogenic or likely pathogenic variant and its cis/trans relationship to the queried variant are documented in the relevant inheritance context; no such evidence is available here.

Evidence considered

• The case bundle provides only the queried NF1 frameshift variant, its predicted protein consequence, ClinVar/gnomAD records, and general NF1 literature; it provides no second variant or phase information.
• The available literature extraction entries do not mention the queried variant and do not report a cis/trans or affected-proband allelic observation relevant to BP2.
• The NF1 specification record is marked as incomplete and has an empty structured rule payload, so no NF1-specific BP2 refinement can be applied from the bundle.

Still missing

• Obtain the proband's complete variant findings and determine whether another pathogenic or likely pathogenic variant is present.
• Obtain validated phase information establishing whether any additional pathogenic variant is in trans or in cis with NM_001042492.3:c.6737del.
• Obtain relevant parental or family testing and phenotype data if BP2 is being considered in an affected individual.

Sources

Reasoning

No individual-level phenotype or molecular testing results identifying an alternative cause of disease were supplied. BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5 requires a variant in a gene for a fully penetrant dominant disorder to be observed in an individual with an alternate molecular basis for disease; no applicable NF1-specific BP5 rule was retrieved from the available CSPEC material.

Still missing

• Provide phenotype and comprehensive molecular results documenting whether an independent molecular diagnosis explains the presentation.