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Variant
Evidence
Report
BLD-0417-031 · tumour vs normal chr4:1,799,300-1,804,300 · FGFR3 · GRCh38 · Mutect2 4.6synthetic Decision support · clinician decides
Variants 42 called · 12 reportable · 4 auto-filtered shown · scored by Evo 2 40B on Civo A100Δ = log-likelihood change, below −2.5 damaging
| Gene | HGVS c. | Protein | Locus GRCh38 | Consequence | VAF | Depth | ClinVar | Evo 2 40B Δ | gnomAD AF | Tier | Review |
|---|---|---|---|---|---|---|---|---|---|---|---|
| FGFR3 | c.746C>G | p.Ser249Cys | 4:1,801,841 | Missense | 0.38 | 1,084 | Pathogenic | -3.92 | 0 | Tier IA | Unreviewed |
| TERT | c.-124C>T | promoter | 5:1,295,113 | Upstream | 0.41 | 896 | Pathogenic | -2.71 | 0 | Tier IIC | Unreviewed |
| KDM6A | c.1663C>T | p.Gln555Ter | X:44,929,412 | Stop gained | 0.44 | 712 | Likely pathogenic | -4.65 | 0 | Tier IIC | Unreviewed |
| ARID1A | c.4001del | p.Gln1334fs | 1:26,779,118 | Frameshift | 0.29 | 801 | Likely pathogenic | -4.11 | 0 | Tier IIC | Unreviewed |
| PIK3CA | c.1633G>A | p.Glu545Lys | 3:179,218,303 | Missense | 0.17 | 943 | Pathogenic | -3.37 | 0 | Tier IIB | Unreviewed |
| STAG2 | c.646C>T | p.Arg216Ter | X:124,034,211 | Stop gained | 0.22 | 655 | Likely pathogenic | -4.48 | 0 | Tier IIC | Unreviewed |
| KMT2D | c.12274C>T | p.Gln4092Ter | 12:49,026,033 | Stop gained | 0.12 | 1,012 | Likely pathogenic | -4.02 | 0 | Tier III | Unreviewed |
| ERBB2 | c.929C>T | p.Ser310Phe | 17:39,707,066 | Missense | 0.06 | 1,150 | Likely pathogenic | -2.88 | 0 | Tier IIB | Unreviewed |
| EP300 | c.4195G>A | p.Asp1399Asn | 22:41,168,573 | Missense | 0.19 | 744 | VUS | -1.94 | 0.00002 | Tier III | Unreviewed |
| CREBBP | c.4336C>T | p.Arg1446Cys | 16:3,738,551 | Missense | 0.09 | 690 | VUS | -2.15 | 0.00001 | Tier III | Unreviewed |
| RB1 | c.1960+1G>A | splice donor | 13:48,456,393 | Splice | 0.07 | 588 | Likely pathogenic | -3.55 | 0 | Tier IIC | Unreviewed |
| ELF3 | c.205G>T | p.Glu69Ter | 1:202,014,630 | Stop gained | 0.11 | 621 | VUS | -3.02 | 0 | Tier III | Unreviewed |
| FGFR3 | c.1953G>A | p.Thr651= | 4:1,803,601 | Synonymous | 0.49 | 1,022 | Benign | -0.04 | 0.0412 | Tier IV | Auto-filtered |
| FGFR3 | c.1186+? | intronic | 4:1,802,410 | Intron | 0.51 | 312 | Benign | -0.02 | 0.6230 | Tier IV | Auto-filtered |
| TP53 | c.215C>G | p.Pro72Arg | 17:7,676,154 | Missense | 0.97 | 1,104 | Benign | -0.11 | 0.6610 | Tier IV | Auto-filtered |
| CDKN1A | c.93C>A | p.Ser31Arg | 6:36,676,460 | Missense | 0.48 | 701 | Benign | -0.08 | 0.0780 | Tier IV | Auto-filtered |
FGFR3 p.Ser249Cys c.746C>GOncogenic
PatientDesmond Pryce syntheticNHS number999 000 0631SpecimenTURBT 30 Sep · 60% tumourTranscriptNM_000142.5 · exon 7Depth1,084 reads · alt 412 · VAF 0.38Strand biasSOR 0.71 · passesNormal0 / 803 alt readsClinVarPathogenic · 4 stars somaticCOSMICCOSV53513891 · 1,236 tumours
Evo 2 40B scoreCivo A100
−3.92Δ log-likelihood · 99th centile damaging
8,192 bp window · run RUN-24116 · model hash 5e1a…c07
Oncogenicity · ClinGen/CGC/VICC10 points
| OS2 · professional guidelines | +4 | |
| OS3 · hotspot, 1,200+ tumours | +4 | |
| OP1 · in silico, Evo 2 and REVEL | +1 | |
| OP4 · absent from gnomAD | +1 |
Timeline12 Oct
| Fri 16:20 Sarek calls 42 variants |
| Fri 16:24 Evo 2 40B scores 42 on Civo A100 |
| 09:05 Jude pre-fills ClinVar, COSMIC, gnomAD |
| 11:12 Opened by Example user |
Next decision
ProposedOncogenic · Tier IAActionFGFR inhibitor eligibilityMDTWed 15 Oct 08:00
ConfirmTo MDT2nd review
Clinical scientist signs · Jude drafts, never decides
Tell Jude what you intend to do
JudeAI · Qwen 27B on Civo