Starting
Initialising…
0%
STAT3
Final classification
VUS
STAT3 c.1940A>T · p.Asn647Ile
STAT3

NM_139276.2:c.1940A>T (p.Asn647Ile) in STAT3 was assessed using generic ACMG/AMP 2015 criteria (PMID:25741868). No CSPEC/VCEP framework is available for STAT3.

Gene
STAT3
Transcript
NM_139276.2
HGVS · transcript:coding
NM_139276.2:c.1940A>T
Consequence
N/A
GRCh38
chr17:42322443 T>A
GRCh37
chr17:40474461 T>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
STAT3 c.1940A>T

NM_139276.2:c.1940A>T (p.Asn647Ile) in STAT3 was assessed using generic ACMG/AMP 2015 criteria (PMID:25741868). No CSPEC/VCEP framework is available for STAT3.1 This missense variant is located in the SH2 domain (residues 583–688), a well-established mutational hotspot where numerous pathogenic variants have been identified in both germline hyper-IgE syndrome and somatic lymphoproliferative disorders, satisfying PM1 at moderate strength.2 The variant is absent from gnomAD v2.1 (0/251,490 alleles) and extremely rare in gnomAD v4.1 (2/1,614,212 alleles; AF=1.24×10⁻⁶), satisfying PM2 at supporting strength.3 In silico predictors do not reach consensus for pathogenicity (REVEL 0.359; BayesDel −0.126; SpliceAI 0.00), and do not reach consensus for benign impact either — PP3 and BP4 are not met.4 ClinVar classification is conflicting: two clinical laboratories report Uncertain Significance and one reports Pathogenic. No expert panel review is available. PP5 is not met due to conflicting interpretations, and BP6 is not met as no submitter classifies the variant as Benign.5 Several criteria (PS3, PS4) could not be fully assessed because variant-specific evidence from cited publications could not be confirmed without full-text access. PMID:27345172 ('Distinct mutations at the same positions of STAT3 cause either loss or gain of function') is of particular relevance for functional evidence but has no abstract or full-text available in the evidence packet. With 1 moderate criterion (PM1) and 1 supporting criterion (PM2) met, and no benign criteria met, the variant does not reach the Likely Pathogenic threshold (requires at least 1 strong + 1–2 moderate, or 3 moderate, or 2 moderate + 2 supporting). The variant is classified as a Variant of Uncertain Significance (VUS) according to generic ACMG/AMP 2015 combination rules.6

PM1 + PM2 VUS
1 generic_acmg_combination_rules
4 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_139276.2 · variants mapped to exon structure
STAT3 NM_139276.2
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 1.23899e-06; MAF= 0.00012%, 2/1614212 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.69488e-06; MAF= 0.00017%, 2/1180028 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/251490 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16256 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00012% · 2 / 1,614,212
      0 hom · FAF 2.8e-05%
      European (non-Finnish)
      2 / 1,180,028
      0.00017%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      Absent · 0 / 251,490
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories) and as Pathogenic (1 clinical laboratory). (ClinVarID = 932423)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.359. BayesDel score = -0.125529.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52882818, n = 28 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      3papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & References.
      STAT3 mutations unify the pathogenesis of chronic lymphoproliferative disorders of NK cells and T-cell large granular lymphocyte leukemia.
      Found
      reports SH2 domain (exons 20-21) as site of recurrent mutations.
      Applied to
      PM1 supports · met
      Distinct mutations at the same positions of STAT3 cause either loss or gain of function.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      Structural Implications of STAT3 and STAT5 SH2 Domain Mutations.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      31002364 ↗ JAK3/STAT3 oncogenic pathway and PRDM1 expression stratify clinicopathologic features of extranodal NK/T‑cell lymphoma, nasal type. CLINVAR
      31278738 ↗ Molecular Genetics in the Diagnosis and Biology of Lymphoid Neoplasms. CLINVAR
      32273478 ↗ Genetic lesions in MYC and STAT3 drive oncogenic transcription factor overexpression in plasmablastic lymphoma. CLINVAR
      33579790 ↗ Oncogenetic landscape of lymphomagenesis in coeliac disease. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR