FGFR4 c.770C>T, p.(Ala257Val)

Reasoning

PM2 is met at supporting strength. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0 and has AC=0/AN=1,601,818 (AF 0) with zero homozygotes in gnomAD v4.1. No population-frequency artifact or ancestry-specific elevation is present in the supplied data.

Rule

Generic ACMG/AMP PM2, supporting strength: absent from population databases or present only at an extremely low frequency not inconsistent with disease.

Evidence considered

• No FGFR4 ClinGen VCEP specification or local gene-specific framework was available; generic ACMG/AMP population-frequency interpretation was used.
• gnomAD v4.1 reports AC=0, AN=1,601,818, AF=0, and zero homozygotes; the highest listed population, African/African American, has AC=0/AN=74,776.
• The variant is reported absent from gnomAD v2.1 and gnomAD-Canada v1.0.

Still missing

• No FGFR4-specific population threshold or disease prevalence/penetrance model was available; the strength is limited to supporting under the generic rarity framework.

Sources

Reasoning

PM1 requires location in a mutational hotspot and/or a well-established critical functional domain lacking benign variation. The cancerhotspots.org lookup for FGFR4 A257 explicitly returned no significant-hotspot row ('This variant does not lie in a statistically significant hotspot'). No residue-level functional-domain annotation (e.g., ligand-binding pocket, kinase active site) placing codon 257 in a critical, well-established domain was retrieved in this case bundle; only gene-level literature description of the FGFR4 extracellular Ig-like domain architecture was found, which is insufficient to establish PM1 at the residue level. No CSPEC/VCEP-specific PM1 hotspot/domain table exists for FGFR4 (cspec.found=false), so generic ACMG criteria were applied.

Evidence considered

• hotspots screenshot/scrape evidence_sentence (cancerhotspots.org, query 'FGFR4 A257'): 'This variant does not lie in a statistically significant hotspot.'
• COSMIC search (COSV52808680) shows only n=1 somatic report, insufficient to establish a recurrent hotspot.
• PMID:23880303 (gene-level review, Kelleher et al., Carcinogenesis 2013): describes FGFR4 as having an extracellular region of three Ig-like domains, a transmembrane segment, and a split intracellular tyrosine kinase domain, but does not mention this variant or map codon 257 to a specific critical functional subdomain — general gene architecture only, not variant-specific, so not usable to support PM1 at the residue level.

Still missing

• No UniProt/structural domain-boundary mapping was retrieved confirming or excluding codon 257 as lying in a critical, well-established functional domain.

Reasoning

NM_213647.2:c.770C>T is a missense substitution (NP_998812.1:p.(Ala257Val)). No FGFR4-specific ClinGen CSPEC/VCEP PP3/BP4 in-silico framework was retrieved for this case (cspec.found=false, gene_vcep_dir=null, vcep_materials note='no cspec url available'), so the lab's generic ACMG/AMP fallback calibration applies. Per that fallback, missense variants are assessed using REVEL only (never combined with the splice-path predictor). REVEL score = 0.396, which falls within the gray zone (0.250-0.750), below the PP3 supporting threshold of >0.750. SpliceAI (max delta = 0.00) is not the governing predictor for this variant type because it is a missense substitution, not an intronic/synonymous/non-canonical-splice-position variant, so its near-zero score is not used to invoke or exclude PP3 here. BayesDel (score -0.167142) has no verified published threshold available to this pipeline and per the generic fallback rule must never be used for PP3/BP4 regardless of any recalled cutoff.

Rule

generic_acmg_pp3_bp4_missense_revel

Evidence considered

• REVEL score for NM_213647.2:c.770C>T / p.(Ala257Val) = 0.396 (source_registry key 'revel'), which lies within the gray zone [0.250, 0.750] defined in the lab's generic ACMG/AMP PP3/BP4 in-silico calibration (generic_acmg_classification_rules.md), so it does not clear the >0.750 threshold required for PP3.
• No FGFR4 VCEP-specific CSPEC PP3/BP4 lookup table was available in vcep_materials.json (cspec.found=false; no cspec url); therefore the generic fallback calibration governs rather than a gene-specific spreadsheet.
• SpliceAI max delta score = 0.00 was retrieved but is not applicable to this missense variant under the generic fallback's variant-type routing rule (missense variants use REVEL only, never combined with the splice-path score).

Still missing

• No gene-specific (FGFR4) ClinGen VCEP PP3/BP4 in-silico specification exists yet; if one is published, REVEL/CSPEC thresholds should be re-applied per that document instead of the generic fallback.

Sources

Reasoning

No exact-variant ClinVar record or expert-panel Pathogenic/Likely pathogenic assertion is present.

Rule

PP5 requires an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary laboratory submissions and aggregate labels are insufficient.

Evidence considered

• ClinVar exact-variant searches for NM_213647.2:c.770C>T returned no result; therefore no expert-panel Pathogenic or Likely pathogenic assertion exists to support PP5.

Sources

Reasoning

BA1 is not met. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0; gnomAD v4.1 reports 0/1,601,818 alleles (AF 0) and 0 homozygotes, with 0/74,776 alleles in the listed highest-frequency African/African American population. These data do not show a stand-alone benign population frequency.

Rule

Generic ACMG/AMP BA1: allele frequency is above the stand-alone benign threshold.

Evidence considered

• No FGFR4 ClinGen VCEP specification or local gene-specific framework was available; generic ACMG/AMP population-frequency interpretation was used.
• gnomAD v4.1 reports AC=0, AN=1,601,818, AF=0, and zero homozygotes; the African/African American population also has AC=0/AN=74,776.
• The variant is reported absent from gnomAD v2.1 and gnomAD-Canada v1.0.

Sources

Reasoning

BS1 is not met. The variant has no observed alleles in gnomAD v4.1 (0/1,601,818; AF 0), gnomAD v2.1, or gnomAD-Canada v1.0, so its frequency cannot exceed an expected disease-compatible frequency.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder.

Evidence considered

• No FGFR4 ClinGen VCEP specification or local gene-specific framework was available; generic ACMG/AMP population-frequency interpretation was used.
• gnomAD v4.1 reports AC=0, AN=1,601,818, AF=0, and zero homozygotes; no subgroup frequency exceeds zero.
• The variant is reported absent from gnomAD v2.1 and gnomAD-Canada v1.0.

Sources

Reasoning

Under the same generic ACMG/AMP fallback calibration (no FGFR4 VCEP-specific PP3/BP4 framework available), missense variants are assessed by REVEL alone. REVEL score = 0.396 falls in the gray zone [0.250, 0.750] and is above the BP4 supporting threshold of <0.250, so BP4 is not met. SpliceAI (max delta = 0.00) is not applicable to this missense variant per the generic fallback's variant-type routing rule, and BayesDel (-0.167142) has no verified published threshold and is therefore not usable for BP4 under this pipeline's current calibration.

Rule

generic_acmg_pp3_bp4_missense_revel

Evidence considered

• REVEL score for NM_213647.2:c.770C>T / p.(Ala257Val) = 0.396 (source_registry key 'revel') lies within the gray zone [0.250, 0.750] of the lab's generic ACMG/AMP PP3/BP4 calibration, above the <0.250 threshold required for BP4.
• No FGFR4 VCEP-specific CSPEC PP3/BP4 lookup table was available (cspec.found=false), so the generic REVEL-only fallback governs this missense variant.
• SpliceAI max delta score = 0.00 was retrieved but not applicable to BP4 assessment here because this is a missense substitution, not an intronic/synonymous/non-canonical-splice-position variant per the fallback's routing rule.

Still missing

• No gene-specific (FGFR4) ClinGen VCEP PP3/BP4 in-silico specification exists yet; re-evaluate against that document's thresholds if/when published.

Sources

Reasoning

No exact-variant ClinVar record or expert-panel Benign/Likely benign assertion is present.

Rule

BP6 requires an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary laboratory submissions and aggregate labels are insufficient.

Evidence considered

• ClinVar exact-variant searches for NM_213647.2:c.770C>T returned no result; therefore no expert-panel Benign or Likely benign assertion exists to support BP6.

Sources

Reasoning

PS1 requires identification of a different nucleotide change producing the identical amino acid change (p.Ala257Val) that has been established as pathogenic. This variant is absent from ClinVar (no submissions), and the pipeline's automated same-residue comparator search explicitly declined to run ('Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting'), so no same-amino-acid-change comparator data was collected for this case.

Evidence considered

• case_summary.json compact_evidence.clinvar.evidence_sentence: 'This variant is absent from ClinVar.'
• pm5_candidates.json: pm5_mode='unknown', eligible_for_classic_pm5_search=false, reason='Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting.' — this scaffold covers same-residue comparator harvesting generally, including the same-amino-acid-change search needed for PS1, and no candidates were collected (candidate_summary.total_candidates_seen=0).

Still missing

• No ClinVar/literature search was performed for other nucleotide substitutions producing p.(Ala257Val) with an established pathogenic classification; this must be done manually before PS1 can be assessed.

Sources

Reasoning

No proband phenotype, parental genotype, parentage confirmation, or de novo testing result is available for NM_213647.2:c.770C>T (p.Ala257Val). PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: a de novo variant in a patient with the disease and no family history, with maternity and paternity confirmed.

Evidence considered

• No FGFR4 VCEP/ClinGen gene-specific specification or local gene-specific framework was retrieved; the case is designated for generic ACMG/AMP fallback.
• The consolidated case-evidence bundle contains no family-based observation, parental testing result, confirmed de novo event, or phenotype information for this variant.

Still missing

• Obtain the proband's phenotype and diagnostic context.
• Obtain testing results for both biological parents, including confirmation of parentage and assessment for parental mosaicism.

Reasoning

No CSPEC/VCEP functional framework is available for FGFR4 (cspec.found=false; vcep_materials empty), so generic ACMG applies. No literature was retrieved (literature_pass total_pmids=0) and fulltext_map is empty, so no validated functional/biochemical assay data (kinase activity, cell proliferation, phosphorylation, or other well-established assay) addressing NM_213647.2:c.770C>T (p.Ala257Val) was found in the case bundle. No functional study evidence exists to assess assay validity, controls, or PS3 strength calibration.

Evidence considered

• literature_pass.json reports total_pmids=0 and note 'No PMIDs found across evidence sources', indicating no functional-assay publications were identified for this variant.
• vcep_materials.json shows no cspec url available and no gene-specific VCEP functional assay framework for FGFR4.
• fulltext_map.json is empty, confirming no full-text papers were mapped for potential functional assay review.

Still missing

• No functional/biochemical assay publications identified or retrieved for this variant
• No CSPEC/VCEP-specific PS3 functional assay framework available for FGFR4
• Selective full-text review under /publications was not warranted because no literature entries reference a functional study for this variant

Reasoning

No affected-case series or case-control dataset reports this exact FGFR4 variant, so case enrichment cannot be evaluated.

Rule

Generic ACMG/AMP 2015 PS4: increased prevalence in affected individuals versus controls must be demonstrated; no FGFR4-specific specification was available.

Evidence considered

• The literature pass contains no PMIDs or variant-specific publications, and the evidence bundle contains no case-control data for NM_213647.2:c.770C>T (p.Ala257Val).

Still missing

• Variant-specific affected and control counts from an ascertainment-defined cohort, with an appropriate statistical enrichment analysis.

Reasoning

PM3 cannot be assessed. No affected-proband observation, second variant, phase result, or evidence of a recessive FGFR4 disease mechanism is present in the consolidated case-evidence bundle.

Rule

Generic ACMG/AMP PM3: in a recessive disorder, the variant is detected in trans with a pathogenic variant.

Evidence considered

• No FGFR4 CSPEC/VCEP framework was retrieved; the case framework specifies generic ACMG/AMP fallback.
• The consolidated literature pass reports zero PMIDs and the fulltext map is empty.
• The consolidated case evidence contains no affected individual carrying NM_213647.2:c.770C>T with another FGFR4 variant, and no phase or segregation data.

Still missing

• Affected-proband genotypes with a confirmed pathogenic/likely pathogenic FGFR4 variant in trans with NM_213647.2:c.770C>T.
• Phase evidence and a substantiated recessive FGFR4 disease/inheritance context.

Sources

Reasoning

PM5 requires a previously established pathogenic variant at the same residue with a different amino acid substitution. The pipeline's PM5 candidate harvesting step was explicitly skipped ('Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting'), yielding zero same-residue candidates (candidate_summary.same_residue_candidates=0). No independent same-residue ClinVar or literature search was performed for this group.

Evidence considered

• pm5_candidates.json: pm5_mode='unknown', eligible_for_classic_pm5_search=false, candidate_summary.same_residue_candidates=0, recommendation.summary='Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting.'

Still missing

• No same-residue (codon 257) alternate-amino-acid comparator search (ClinVar/literature) has been performed; required before PM5 can be assessed.

Sources

Reasoning

No report identifies the variant as de novo without confirmed parentage; PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence without confirmation of paternity and maternity.

Evidence considered

• No FGFR4 VCEP/ClinGen gene-specific specification or local gene-specific framework was retrieved; the case is designated for generic ACMG/AMP fallback.
• The consolidated case-evidence bundle contains no family-based observation, parental testing result, reported de novo event, or phenotype information for this variant.

Still missing

• Obtain parental genotypes demonstrating absence of the variant in both parents.
• Document whether biological parentage was confirmed; if it was not, document the de novo observation and phenotype context.

Reasoning

No affected relatives, genotypes, phenotypes, or informative meioses are reported. PP1 cannot be assessed.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No FGFR4 VCEP/ClinGen gene-specific specification or local gene-specific framework was retrieved; the case is designated for generic ACMG/AMP fallback.
• The consolidated case-evidence bundle contains no pedigree, familial genotyping, phenotype co-segregation data, or informative meioses for this variant.

Still missing

• Obtain a pedigree with phenotype status and FGFR4 genotype for affected and unaffected informative relatives.
• Document the number of informative segregations/meioses and any relevant age-dependent penetrance considerations.

Reasoning

PP2 requires that the gene have a low rate of benign missense variation and that missense be an established mechanism of disease for the relevant phenotype. No missense-constraint metric (e.g., gnomAD missense Z-score/O:E) or curated missense-mechanism statement is present in this case bundle: the custom_pp2_score field is null and no hci_prior/MAPP data was retrieved. FGFR4's disease mechanisms in the literature are mixed and residue-context dependent (somatic gain-of-function activating mutations in cancer vs. the gene-context note's claim of a germline loss-of-function mechanism for a pituitary-adenoma phenotype), so no single, well-established missense-as-primary-mechanism conclusion could be drawn from the assembled evidence without further targeted review. No CSPEC/VCEP-specific PP2 gene list applies (cspec.found=false).

Evidence considered

• evidence.json compact predictor block: hci_prior.custom_pp2_score = null (no locally available PP2-style missense constraint score).
• PMID:23880303 (gene-level review): notes FGFR family somatic mutations in cancer are generally gain-of-function, while germline FGFR mutations cause developmental syndromes — a general statement about missense pathogenicity across the FGFR family, not a residue- or gene-specific missense-constraint statistic usable to satisfy PP2 for FGFR4 specifically.

Still missing

• No gnomAD missense constraint (Z-score/O:E) or ClinGen curated missense-mechanism statement for FGFR4 was retrieved in this bundle.

Reasoning

No proband phenotype, diagnostic work-up, or phenotype-specificity evidence is supplied for this variant.

Rule

Generic ACMG/AMP 2015 PP4: apply only when the patient's phenotype or family history is highly specific for a disease with a single genetic etiology; no FGFR4-specific specification was available.

Evidence considered

• The consolidated case evidence provides no individual phenotype or phenotype-to-gene correlation for NM_213647.2:c.770C>T (p.Ala257Val).

Still missing

• Proband phenotype and diagnostic evaluation.
• Evidence that the observed phenotype is highly specific for an FGFR4-associated Mendelian disorder and has a low alternative diagnostic yield.

Reasoning

BS2 is not assessed. There are no observed gnomAD homozygotes (and no observed alleles), and the case bundle provides no phenotype-verified healthy adult carriers or penetrance/age-of-onset evidence needed to establish that a carrier is unaffected for an FGFR4-related disorder.

Rule

Generic ACMG/AMP BS2: observed in a healthy adult individual for a disorder expected to be fully penetrant at an early age.

Evidence considered

• gnomAD v4.1 reports zero homozygotes and zero alternate alleles; absence of carriers cannot supply BS2 evidence.
• No FGFR4 ClinGen VCEP specification or local gene-specific framework was available.

Still missing

• Phenotype-verified healthy adult carrier observations with age and relevant disease context are needed for BS2.
• FGFR4 disease validity, inheritance, penetrance, and age-of-onset information applicable to this variant remain unavailable in the provided evidence.

Sources

Reasoning

No CSPEC/VCEP functional framework is available for FGFR4, and no literature or full-text sources were retrieved in this case bundle (literature_pass total_pmids=0; fulltext_map empty). No functional/biochemical assay data showing normal/wild-type-like activity for NM_213647.2:c.770C>T (p.Ala257Val) was found, so BS3 cannot be assessed.

Evidence considered

• literature_pass.json reports total_pmids=0 and note 'No PMIDs found across evidence sources', indicating no functional-assay publications were identified for this variant.
• vcep_materials.json shows no cspec url available and no gene-specific VCEP functional assay framework for FGFR4.

Still missing

• No functional/biochemical assay publications identified or retrieved for this variant
• No CSPEC/VCEP-specific BS3 functional assay framework available for FGFR4

Reasoning

No informative family data show lack of segregation between the variant and a relevant phenotype. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family.

Evidence considered

• No FGFR4 VCEP/ClinGen gene-specific specification or local gene-specific framework was retrieved; the case is designated for generic ACMG/AMP fallback.
• The consolidated case-evidence bundle contains no pedigree, familial genotyping, phenotype non-segregation data, or informative meioses for this variant.

Still missing

• Obtain genotype and phenotype data from informative relatives, including affected non-carriers or unaffected carriers where interpretation is valid.
• Document penetrance, age of onset, and phenotyping adequacy before treating an apparent non-segregation observation as evidence.

Reasoning

BP1 requires that the gene's disease mechanism be primarily truncating/loss-of-function such that a missense variant is less likely pathogenic. No formal gene-level curation of the missense-vs-truncating disease-mechanism split for FGFR4 germline disease was retrieved in this bundle. The pvs1_gene_context.json note asserts literature-only support for a germline loss-of-function mechanism relevant to a pituitary-adenoma phenotype, but this was collected specifically to gate PVS1 (null-variant) applicability, not to characterize the relative frequency of truncating vs. missense pathogenic variants in FGFR4, and is confounded by the well-documented gain-of-function missense mechanism of FGFR4 in somatic cancer contexts. This is insufficiently dispositive to apply BP1 either way.

Evidence considered

• pvs1_gene_context.json: mechanism_rationale describes literature-only support for a germline LOF mechanism (used for PVS1 gating), which is not a direct BP1-qualifying statement about missense-vs-truncating variant proportions and is not treated as one here.
• PMID:23880303: notes FGFR somatic mutations in cancer are generally gain-of-function missense changes, which argues against treating FGFR4 as a gene where disease is primarily caused by truncating variants, but this gene-level statement alone is not sufficient to affirmatively resolve BP1.

Still missing

• No curated statement on the relative proportion of truncating vs. missense pathogenic variants in FGFR4 germline disease was retrieved.

Reasoning

BP2 cannot be assessed. The consolidated case-evidence bundle contains no co-occurrence observation of NM_213647.2:c.770C>T with a pathogenic/likely pathogenic variant, no cis/trans phase information, and no adequately established fully penetrant dominant FGFR4 disease context for this use of BP2.

Rule

Generic ACMG/AMP BP2: observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• No FGFR4 CSPEC/VCEP framework was retrieved; the case framework specifies generic ACMG/AMP fallback.
• The consolidated literature pass reports zero PMIDs and the fulltext map is empty.
• The consolidated case evidence contains no reported co-occurrence, phase result, or pedigree/inheritance data for NM_213647.2:c.770C>T.

Still missing

• A documented co-occurrence with a pathogenic/likely pathogenic variant in the same individual, including phase when relevant.
• Evidence that the relevant FGFR4 disorder is fully penetrant and dominant if BP2 is considered on the basis of a trans co-occurrence.

Sources

Reasoning

No proband-level molecular results or established alternative genetic cause are supplied.

Rule

Generic ACMG/AMP 2015 BP5: apply only when a variant is found in a case with an alternate molecular basis for disease; no FGFR4-specific specification was available.

Evidence considered

• The consolidated case evidence contains no patient genotype, phenotype, or alternate molecular diagnosis for assessment of BP5.

Still missing

• A confirmed pathogenic or likely pathogenic molecular diagnosis that fully explains the proband's phenotype, together with phenotype correlation.