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ROS1
Final classification
VUS
ROS1 c.6609C>A · p.Asp2203Glu
ROS1

NM_002944.2:c.6609C>A (p.Asp2203Glu) is a rare missense variant in ROS1, present in gnomAD v4.1 at extremely low frequency (AF=2.50×10⁻⁶, 4/1,600,906 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada, meeting PM2 at supporting level.

Gene
ROS1
Transcript
NM_002944.2
HGVS · transcript:coding
NM_002944.2:c.6609C>A
Consequence
N/A
GRCh38
chr6:117301098 G>T
GRCh37
chr6:117622261 G>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, BP4 supporting; combination = 1 supporting + 1 supporting benign, 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, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
ROS1 c.6609C>A

NM_002944.2:c.6609C>A (p.Asp2203Glu) is a rare missense variant in ROS1, present in gnomAD v4.1 at extremely low frequency (AF=2.50×10⁻⁶, 4/1,600,906 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada, meeting PM2 at supporting level.1 Multiple in silico tools predict a benign effect: REVEL score is 0.14, BayesDel score is −0.455671, and SpliceAI predicts no splice impact (max delta=0.01). Additionally, the substitution is biochemically conservative (Asp→Glu, both acidic residues), meeting BP4 at supporting level.2 This variant is absent from ClinVar with no clinical assertions, has not been reported in COSMIC, does not lie in a statistically significant mutational hotspot, and has no variant-specific functional evidence (OncoKB: Unknown Oncogenic Effect). No publications mention this specific variant.3 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is balanced. No other criteria are met. This variant is classified as a Variant of Uncertain Significance (VUS) under ACMG/AMP 2015 generic framework.4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002944.2 · variants mapped to exon structure
ROS1 NM_002944.2
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= 2.49859e-06; MAF= 0.00025%, 4/1600906 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.34055e-05; MAF= 0.00134%, 1/74596 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
      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
      0.00025% · 4 / 1,600,906
      0 hom · FAF 6.8e-05%
      African/African American
      1 / 74,596
      0.0013%
      European (non-Finnish)
      3 / 1,174,998
      0.00026%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      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 = 0.01). REVEL score = 0.14. BayesDel score = -0.455671.
      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. ROS1, a receptor tyrosine kinase, is altered by mutation or chromosomal rearrangement in a diverse range of cancers, including lung cancer.
      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 not previously been reported in somatic cancers (COSMIC).
      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