FGFR3 c.1959C>T, p.(Asn653=)

Reasoning

PM2 is met at supporting strength under the generic operating threshold because the variant is rare in population databases: overall AF is 0.00174% in gnomAD v4.1 and the highest ancestry-specific AF is 0.09862%, both below 0.1%, with zero homozygotes. The ancestry-specific value is close to the cutoff and is based on only 6 alleles, so the PM2 call warrants human review for threshold and ancestry-sampling artifacts.

Rule

Generic PM2 operating threshold: allele frequency <0.1% with no homozygotes; no applicable FGFR3 VCEP/CSPEC was retrieved. Human review is indicated because the maximum ancestry-specific frequency is close to the cutoff.

Evidence considered

• gnomAD v4.1 reports 28/1,612,632 alleles, overall AF 1.73629e-05 (0.00174%), zero homozygotes, and maximum group AF 0.00042888.
• The highest v4.1 ancestry-specific value is 6/6084 Middle Eastern alleles, AF 0.000986193 (0.09862%), just below the generic PM2 cutoff of 0.1%; no homozygotes were observed in that population.
• gnomAD v2.1 reports 7/248,438 alleles, overall AF 2.8176e-05 (0.00282%), zero homozygotes, and grpmax FAF 7.13e-06.
• gnomAD-Canada v1.0 reports the variant absent, providing concordant rarity evidence but not evidence of complete absence from all populations.

Still missing

• No FGFR3-specific population-frequency or PM2 specification was retrieved.
• The highest ancestry-specific frequency is near the generic 0.1% cutoff and is based on a small Middle Eastern allele count (6/6084).
• Disease prevalence, penetrance, and an independently derived maximum credible allele frequency were not provided.

Sources

Reasoning

No VCEP/CSPEC framework was retrieved for FGFR3, so the lab's generic ACMG/AMP fallback PP3/BP4 calibration rule applies. NM_000142.4:c.1959C>T is a synonymous substitution (not missense), so per the generic rule the applicable predictor is SpliceAI, not REVEL. SpliceAI Lookup returned max delta score = 0.00, below the BP4 threshold of <0.1 for non-missense variants, indicating no predicted splice impact. BP4 (supporting, benign) is met on this basis.

Rule

Generic ACMG fallback PP3/BP4 in-silico calibration (non-missense path): SpliceAI max delta < 0.1 -> BP4 supporting.

Evidence considered

• SpliceAI Lookup for NM_000142.4:c.1959C>T (hg37) returned max delta score = 0.00 (pangolin_SG=0.052, pangolin_SL=-0.006), below the generic fallback's BP4 threshold of <0.1 for synonymous/intronic/non-canonical-splice variants, supporting no predicted splice impact.
• No BayesDel evidence was used: per pipeline calibration policy, BayesDel has no verified published threshold available and is never usable for PP3/BP4 regardless of any recalled cutoff.

Sources

Reasoning

No VCEP/CSPEC was retrieved for FGFR3 (cspec.found=false; vcep_materials.final_classification_framework.found=false, source='generic_acmg_fallback'), so the lab's generic ACMG/AMP fallback rule applies. NM_000142.4:c.1959C>T is a synonymous substitution (NP_000133.1:p.(Asn653=)), not a missense change, so REVEL is not the applicable predictor (and REVEL was in fact not found/scored for this variant - revel.found=false, revel_score=null). Under the generic rule's non-missense (intronic/synonymous/non-canonical-splice) path, SpliceAI is the applicable predictor. SpliceAI Lookup returned max delta score = 0.00 (pangolin_SG=0.052, pangolin_SL=-0.006, max_delta_score=0), well below the PP3 threshold of >0.2. PP3 is therefore not met.

Rule

Generic ACMG fallback PP3/BP4 in-silico calibration (non-missense path): SpliceAI max delta > 0.2 -> PP3 supporting.

Evidence considered

• SpliceAI Lookup for NM_000142.4:c.1959C>T (hg37) returned max delta score = 0.00, well under the generic fallback's PP3 threshold of >0.2 for non-missense (synonymous/intronic) variants.
• Variant is synonymous (p.(Asn653=)), so the missense REVEL path is not applicable; REVEL score was also not available for this variant per prefetch (found=false).

Sources

Reasoning

PP5 is not met. The exact ClinVar record for NM_000142.4:c.1959C>T has one clinical-laboratory submission classified as Uncertain significance with criteria provided and single-submitter review status; there is no expert-panel Pathogenic or Likely pathogenic assertion. Ordinary laboratory submissions and an aggregate ClinVar label do not qualify for PP5.

Rule

Apply PP5 only when an exact-variant ClinVar expert-panel assertion is Pathogenic or Likely pathogenic; non-expert laboratory submissions, aggregate labels, and other assertions are excluded.

Evidence considered

• ClinVar variation 2068953 is an exact match to NM_000142.4:c.1959C>T and reports Uncertain significance, criteria provided, single submitter, with one clinical-laboratory submission and zero expert-panel submissions.
• The cited PMID:28492532 is attached to the laboratory submission, not an expert-panel assertion, and cannot trigger PP5.

Sources

Reasoning

BA1 is not met. The highest reported gnomAD v4.1 ancestry-specific allele frequency is 0.09862% in the Middle Eastern population (6/6084 alleles), well below the generic 1% BA1 threshold; the overall frequency is 0.00174% (28/1,612,632 alleles).

Rule

Generic BA1 threshold: allele frequency >1%; no applicable FGFR3 VCEP/CSPEC was retrieved.

Evidence considered

• gnomAD v4.1 reports 28/1,612,632 alleles, overall AF 1.73629e-05 (0.00174%), with no homozygotes.
• The highest v4.1 population-specific AF is 6/6084 alleles in the Middle Eastern population, 0.000986193 (0.09862%), which is below 1%.
• gnomAD v2.1 is concordant: 7/248,438 alleles, overall AF 2.8176e-05 (0.00282%), with no homozygotes; highest listed subgroup AF is 0.03296% in Remaining individuals.

Sources

Reasoning

BS1 is not met. The maximum observed population frequency is 0.09862% in gnomAD v4.1, below the generic 0.3% BS1 threshold. The overall frequency is substantially lower at 0.00174%.

Rule

Generic BS1 threshold: allele frequency >0.3%; no applicable FGFR3 VCEP/CSPEC was retrieved.

Evidence considered

• gnomAD v4.1 reports overall AF 1.73629e-05 (0.00174%) and a highest ancestry-specific AF of 0.000986193 (0.09862%) in the Middle Eastern population.
• The v4.1 maximum group frequency is based on 6/6084 alleles and remains below 0.3%; no population frequency exceeds the BS1 threshold.
• gnomAD v2.1 also remains below threshold, with overall AF 2.8176e-05 and highest listed subgroup AF 0.03296%.

Sources

Reasoning

BP6 is not met. The exact ClinVar record for NM_000142.4:c.1959C>T has no expert-panel Benign or Likely benign assertion; the only submission is a single clinical-laboratory Uncertain significance assertion. Ordinary laboratory submissions and aggregate ClinVar labels do not qualify for BP6.

Rule

Apply BP6 only when an exact-variant ClinVar expert-panel assertion is Benign or Likely benign; non-expert laboratory submissions, aggregate labels, and other assertions are excluded.

Evidence considered

• ClinVar variation 2068953 is an exact match to NM_000142.4:c.1959C>T and reports Uncertain significance, criteria provided, single submitter, with one clinical-laboratory submission and zero expert-panel submissions.
• The available ClinVar record contains neither an expert-panel Benign nor an expert-panel Likely benign classification, so BP6 cannot be applied.

Sources

Reasoning

PS2 requires a confirmed de novo occurrence in the proband, ideally established by testing both biological parents, with phenotype consistency and adequate confirmation of parentage. The case-evidence bundle contains no proband genotype description beyond the variant record, no parental testing results, no pedigree or parentage information, no phenotype details, and no meiosis or de novo case report for NM_000142.4:c.1959C>T. Therefore PS2 cannot be assessed.

Rule

generic ACMG/AMP PS2: confirmed de novo variant in an affected proband with confirmed parentage; parental testing and phenotype consistency are required to establish the evidence.

Evidence considered

• The bundle reports no CSPEC/VCEP specification for FGFR3 and falls back to generic ACMG/AMP assessment.
• The consolidated bundle contains no documented proband-parent trio testing, parental genotypes, parentage confirmation, pedigree, phenotype, or de novo observation for this variant.

Still missing

• Proband phenotype and clinical indication are not provided.
• Both biological parents' variant testing results are not provided.
• Parentage and testing methodology/confirmation are not provided.
• No de novo observation with relevant phenotype and segregation context is documented.

Sources

Reasoning

No FGFR3-specific VCEP specification is available for this variant (cspec.found = false), so generic ACMG/AMP applies. No functional/splicing assay data (e.g., minigene, RT-PCR/RNA study, biochemical or cell-based FGFR3 activity assay) for NM_000142.4:c.1959C>T (p.Asn653=, a synonymous change) was found in the case bundle. The literature packet returned zero high/medium priority papers and an empty criteria_index, and no publications directory content was flagged as relevant to functional evidence. SpliceAI predicts no splice impact (max delta = 0.00), but this in-silico prediction is not itself a validated functional assay and does not satisfy PS3.

Still missing

• No published or unpublished functional assay (splicing minigene, RT-PCR patient RNA, protein activity assay) identified for this variant.
• No VCEP-specific functional evidence table available for FGFR3.
• literature_pass.json returned no high or medium priority functional papers to evaluate.

Reasoning

No case-control enrichment data or adequately documented affected-case series for the exact NM_000142.4:c.1959C>T variant were provided in the evidence bundle. PS4 cannot be assessed from population frequency, ClinVar status, or non-variant-specific cancer resources.

Rule

Generic ACMG/AMP PS4 requires a statistically significant enrichment of the variant in affected individuals compared with controls; no applicable VCEP specification was retrieved.

Evidence considered

• The consolidated bundle contains no PS4-indexed literature, affected-case series, or case-control dataset for NM_000142.4:c.1959C>T.
• OncoKB provides only non-variant-specific FGFR3 context and labels the variant-specific oncogenic effect as unknown; this is not evidence for PS4.

Still missing

• Exact-variant affected-case counts and an appropriate control comparison are unavailable.
• No statistically interpretable case-control enrichment analysis is available.

Reasoning

No applicable FGFR3 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP PM3 concept was considered. The case-evidence bundle contains no affected-proband observations, second pathogenic or likely pathogenic allele, phase information, or inheritance-mode evidence establishing biallelic disease. PM3 therefore cannot be applied.

Rule

Generic ACMG/AMP PM3 requires a variant observed in trans with a pathogenic variant in an affected individual, with strength dependent on the number and quality of independent observations; no qualifying observation is available here.

Evidence considered

• The consolidated case-evidence bundle reports no ClinGen CSPEC/VCEP or gene-specific framework for FGFR3.
• The consolidated case-evidence bundle provides only the target variant NM_000142.4:c.1959C>T (p.Asn653=) and contains no family, proband, compound-heterozygous, phase, or allele-pair observations.
• The available ClinVar record is a single-submitter uncertain-significance record and does not provide allelic or phasing evidence for PM3.

Still missing

• Affected-proband case observations are not available.
• No pathogenic or likely pathogenic second FGFR3 variant is documented.
• Phase (trans versus cis) is not documented.
• The relevant disease inheritance mode for applying PM3 is not documented in the case evidence.

Reasoning

PM6 requires a presumed de novo occurrence when parental testing is incomplete or unavailable, supported by a compatible phenotype and credible case documentation. The case-evidence bundle contains no clinical phenotype, pedigree, parental testing limitations, or published case report documenting NM_000142.4:c.1959C>T as presumed de novo. The variant is synonymous, but no evidence is provided that it causes a relevant phenotype or that it arose de novo. Therefore PM6 cannot be assessed.

Rule

generic ACMG/AMP PM6: presumed de novo variant without confirmed parental testing, supported by compatible phenotype and reliable case documentation.

Evidence considered

• The bundle reports no CSPEC/VCEP specification for FGFR3 and falls back to generic ACMG/AMP assessment.
• The literature pass contains no screened segregation or case-observation evidence, and the bundle provides no parental or pedigree data for this variant.

Still missing

• No presumed-de-novo case observation is documented.
• No proband phenotype or phenotype consistency assessment is provided.
• No information is provided about whether parental testing was incomplete or unavailable.
• No pedigree, parentage, or meiosis context is provided.

Sources

Reasoning

PP1 requires co-segregation of the variant with disease in affected family members, with strength determined by the number and informativeness of meioses and the quality of phenotype classification. The case-evidence bundle contains no family pedigree, affected relatives, unaffected relatives, variant genotypes, phenotype assessments, or informative meioses. No segregation publication relevant to NM_000142.4:c.1959C>T was identified in the provided literature packet. Therefore PP1 cannot be assessed at supporting, moderate, or strong strength.

Rule

generic ACMG/AMP PP1: variant co-segregates with disease in affected family members; strength depends on the number and informativeness of meioses and phenotype specificity.

Evidence considered

• The bundle reports no CSPEC/VCEP specification for FGFR3 and falls back to generic ACMG/AMP assessment.
• The literature pass has an empty segregation/case-observation criteria index and provides no family-level segregation data for this variant.

Still missing

• No affected relatives or family pedigree are documented.
• No familial variant genotypes are documented.
• No phenotype consistency assessment for relatives is documented.
• No count or quality assessment of informative meioses is available.

Sources

Reasoning

The case bundle does not provide a clinical phenotype or phenotype-to-disease specificity assessment for the individual carrying NM_000142.4:c.1959C>T. PP4 therefore cannot be assessed.

Rule

Generic ACMG/AMP PP4 requires a highly specific phenotype or family history for the disease associated with the gene; no applicable VCEP specification was retrieved.

Evidence considered

• The consolidated bundle provides variant normalization and database results but no patient phenotype, clinical synopsis, or phenotype specificity analysis.

Still missing

• Detailed patient phenotype and diagnostic features are unavailable.
• The specificity of the phenotype for an FGFR3-related disorder is not documented.

Reasoning

BS2 was not assessed because the bundle contains no disease-focused cohort or validated clinical observation demonstrating this variant in unaffected adults, nor a sufficiently characterized homozygous observation. gnomAD reports zero homozygotes, but population-database presence alone is not sufficient to establish the BS2 unaffected-individual criterion.

Rule

Generic BS2 requires observation in healthy adults or unaffected individuals in a relevant disease context; database carrier presence without phenotype ascertainment is insufficient.

Evidence considered

• gnomAD v4.1 reports zero homozygotes, but the bundle does not provide phenotype or age information for carriers and therefore does not establish BS2.
• gnomAD v2.1 likewise reports zero homozygotes; no unaffected-adult clinical cohort for the exact variant is available in the case bundle.

Still missing

• No phenotype-ascertained healthy-adult cohort or clinical series for the exact variant was provided.
• No evidence establishing unaffected status, age-related penetrance, or homozygous tolerance for this exact variant was provided.

Sources

Reasoning

No FGFR3-specific VCEP specification is available for this variant (cspec.found = false), so generic ACMG/AMP applies. No functional/splicing assay data demonstrating a benign/wild-type-like effect for NM_000142.4:c.1959C>T was found in the case bundle. The literature packet returned zero high/medium priority papers and an empty criteria_index. While SpliceAI predicts no significant splice impact (max delta = 0.00), an in-silico splice prediction is not a validated functional assay and cannot itself establish BS3.

Evidence considered

• SpliceAI (source_registry key: spliceai) predicts no significant splice impact for c.1959C>T (max delta score = 0.00; pangolin_SG=0.052, pangolin_SL=-0.006), consistent with, but not sufficient on its own to establish, a benign splicing effect since it is a computational prediction rather than an experimental functional assay.

Still missing

• No published or unpublished functional/splicing assay result available showing no damaging effect for this variant.
• No RNA-level (e.g., RT-PCR) confirmation of normal splicing for this synonymous variant was located.
• No VCEP-specific functional evidence table available for FGFR3.

Reasoning

BS4 requires lack of segregation in affected family members, with reliable phenotype assessment and informative familial testing. The case-evidence bundle contains no affected relatives, family pedigree, familial variant testing, phenotype classification, or non-segregation observation. Absence of documented segregation data is not evidence that the variant fails to segregate. Therefore BS4 cannot be assessed.

Rule

generic ACMG/AMP BS4: lack of segregation in affected family members, established using reliable phenotype classification and informative familial testing.

Evidence considered

• The bundle reports no CSPEC/VCEP specification for FGFR3 and falls back to generic ACMG/AMP assessment.
• The consolidated bundle contains no non-segregation, affected-relative, pedigree, or familial testing evidence for this variant.

Still missing

• No affected family members with documented negative variant testing are provided.
• No pedigree or phenotype classification is provided.
• No familial testing methodology or informative meiosis count is provided.
• No published non-segregation observation for this variant is documented.

Sources

Reasoning

No applicable FGFR3 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP BP2 concept was considered. The case-evidence bundle contains no pathogenic variant in the same individual, no cis/trans phase result, and no inheritance or clinical observation that could establish the benign allelic relationship required for BP2.

Rule

Generic ACMG/AMP BP2 requires an appropriate observation of the variant with a pathogenic allele in cis or trans according to the disease inheritance model; no qualifying allelic observation is available here.

Evidence considered

• The consolidated case-evidence bundle reports no ClinGen CSPEC/VCEP or gene-specific framework for FGFR3.
• The consolidated case-evidence bundle contains no documented pathogenic comparator allele, phase result, or family inheritance observation for NM_000142.4:c.1959C>T.
• The available ClinVar record is a single-submitter uncertain-significance record and does not provide evidence for BP2.

Still missing

• A second pathogenic or likely pathogenic variant in the individual is not documented.
• Phase (cis or trans) is not documented.
• Inheritance mode and the relevant disease model are not documented for this case.
• No affected-proband or family-level allelic observation is available.

Reasoning

No credible alternative molecular explanation for the patient's phenotype is documented, and no patient phenotype is available against which an alternative diagnosis could be evaluated. BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5 requires a pathogenic variant in another gene that explains the phenotype; no applicable VCEP specification was retrieved.

Evidence considered

• The bundle contains no clinical phenotype, competing pathogenic variant, or alternative molecular diagnosis for this case.
• Non-variant-specific FGFR3 cancer context and absence from COSMIC do not establish an alternative explanation for a germline phenotype.

Still missing

• Patient phenotype and established or suspected alternative diagnosis are unavailable.
• No evidence links an alternative pathogenic variant or condition to the case phenotype.

Reasoning

NM_000142.4:c.1959C>T is a synonymous variant (p.(Asn653=)), the class BP7 is designed for. Standard ACMG/AMP BP7 requires both (a) computational evidence of no predicted splice impact and (b) the substituted nucleotide not being highly conserved across species. The bundle contains no conservation metric (GERP, phyloP, or similar) for this position, only the SpliceAI splice-impact score. That same SpliceAI signal (max delta = 0.00) has already been credited to BP4 above under the generic fallback's explicit synonymous-variant rule; re-applying it to independently satisfy BP7 would double-count the identical prediction across BP4 and BP7, which this group's instructions prohibit. Because the second required component (lack of high conservation) is not available in this bundle and the splice-negative signal is already accounted for elsewhere, BP7 cannot be independently assessed.

Evidence considered

• SpliceAI max delta score = 0.00 for this synonymous variant was already used to satisfy BP4 under the generic non-missense fallback rule; applying it again for BP7 without independent conservation data would double-count the same prediction.

Still missing

• No nucleotide conservation score (e.g. GERP++, phyloP) is present anywhere in the evidence bundle to evaluate the conservation prong of BP7 for this synonymous position.
• This case has no VCEP/CSPEC-specific BP7 rule (framework_mode=generic_acmg, cspec.found=false) that might define an alternate, splice-score-only BP7 threshold distinct from the SpliceAI evidence already applied to BP4.