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JAK1
Final classification
VUS
JAK1 c.1909G>A · p.Glu637Lys
JAK1

NM_002227.3:c.1909G>A (p.Glu637Lys) is extremely rare in population databases, present in gnomAD v4.1 at an allele frequency of 1.24e-06 (2/1,613,736 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada v1.0. This meets PM2 at the supporting level.

Gene
JAK1
Transcript
NM_002227.3
HGVS · transcript:coding
NM_002227.3:c.1909G>A
Consequence
N/A
GRCh38
chr1:64846727 C>T
GRCh37
chr1:65312410 C>T
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: PM2 supporting, PP3 supporting; combination = 2 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: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
JAK1 c.1909G>A

NM_002227.3:c.1909G>A (p.Glu637Lys) is extremely rare in population databases, present in gnomAD v4.1 at an allele frequency of 1.24e-06 (2/1,613,736 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada v1.0. This meets PM2 at the supporting level.1 Computational evidence supports a deleterious effect: REVEL predicts a damaging score of 0.762, meeting PP3 at the supporting level under generic ACMG/AMP guidelines. SpliceAI predicts no splicing impact (max delta=0.00).2 This variant is a missense substitution (p.Glu637Lys) and does not meet PVS1 null-variant criteria. No functional studies, segregation data, de novo observations, case-control data, or prior clinical classifications are available. The variant has been reported in COSMIC (COSV61089427, n=2) in a somatic context but lacks germline disease association evidence.3 Only two supporting-level pathogenic criteria are met (PM2_supporting, PP3_supporting). No moderate, strong, or very strong pathogenic criteria are met. No benign criteria are met. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), two supporting criteria are insufficient to reach Likely Pathogenic (minimum: 1 strong + 2 supporting, or 2 moderate + 2 supporting, or 3 moderate, etc.). The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + PP3 VUS
2 revelspliceai ↗
3 pvs1_variant_assessmentclinvar ↗oncokb ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002227.3 · variants mapped to exon structure
JAK1 NM_002227.3
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= 1.23936e-06; MAF= 0.00012%, 2/1613736 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.6e-05; MAF= 0.00160%, 1/62500 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00012% · 2 / 1,613,736
      0 hom
      Remaining individuals
      1 / 62,500
      0.0016%
      European (non-Finnish)
      1 / 1,179,796
      8.5e-05%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.762. BayesDel score = 0.267658.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. JAK1, an intracellular kinase, is frequently altered in hematologic malignancies and gynecological cancers.
      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; COSV61089427, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots