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ROS1
Final classification
VUS
ROS1 c.6079G>A · p.Glu2027Lys
ROS1

NM_002944.2:c.6079G>A (p.Glu2027Lys) is a rare missense variant in the ROS1 gene, absent from all gnomAD population databases (v2.1, v4.1, gnomAD-Canada).

Gene
ROS1
Transcript
NM_002944.2
HGVS · transcript:coding
NM_002944.2:c.6079G>A
Consequence
N/A
GRCh38
chr6:117317199 C>T
GRCh37
chr6:117638362 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
ROS1 c.6079G>A

NM_002944.2:c.6079G>A (p.Glu2027Lys) is a rare missense variant in the ROS1 gene, absent from all gnomAD population databases (v2.1, v4.1, gnomAD-Canada).1 In silico analysis predicts a deleterious effect: REVEL score 0.923 (strongly pathogenic), BayesDel score 0.4228 (moderately pathogenic). SpliceAI predicts no splice impact (max delta 0.15).2 This variant has been reported once in COSMIC (COSV107471754) as a somatic alteration and is classified as Uncertain Significance in ClinVar (VariationID 2443073, 1 submitter, no assertion criteria provided).3 No variant-specific functional studies, case-control data, segregation data, or de novo observations were identified. OncoKB reports Unknown Oncogenic Effect.4 Under generic ACMG/AMP 2015 criteria, this variant meets PM2 (supporting: absent from population databases) and PP3 (supporting: in silico prediction of deleterious effect). All other assessed criteria are not met or not applicable.5 With two supporting-level pathogenic criteria (PM2_supporting + PP3_supporting) and no benign criteria met, the evidence is insufficient to classify this variant as likely pathogenic. The variant remains a Variant of Uncertain Significance per ACMG/AMP 2015 classification rules (PMID:25741868).6

PM2 + PP3 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
6 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
      Absent from gnomAD v4.1.
      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
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 2443073)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.15). REVEL score = 0.923. BayesDel score = 0.4228.
      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 previously been reported in somatic cancers (COSMIC; COSV107471754, n = 1 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