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ROS1
Final classification
VUS
PM2PP3
ROS1
c.6079G>A
p.Glu2027Lys
This variant

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).

Transcript
NM_002944.2
HGVS · transcript:coding
NM_002944.2:c.6079G>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 applied · 18 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_002944.2:c.6079G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, consistent with a rare variant not observed in large population cohorts. Under generic ACMG/AMP rules, absence from population databases supports PM2 at supporting level.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0 (genomes).
PP3 supporting Pathogenic
REVEL predicts a damaging score of 0.923 for NM_002944.2:c.6079G>A (p.Glu2027Lys), well above the 0.75 threshold for pathogenic prediction. BayesDel score of 0.4228 provides moderate additional support. SpliceAI predicts no splice impact (max delta 0.15). The preponderance of in silico evidence supports a deleterious effect.
REVEL: 0.923 (strongly pathogenic prediction).BayesDel: 0.4228 (moderate pathogenic prediction).SpliceAI: max delta 0.15 (no splice impact
Assessed · not applied · 18 not met · 0 not assessed
Pathogenic
PS2 No de novo observation has been reported for NM_002944.2:c.6079G>A.
PS3 No variant-specific functional studies were identified.
PS4 No case-control studies demonstrating enrichment of NM_002944.2:c.6079G>A in affected individuals versus controls are available.
PM1 Position 2027 does not lie within a statistically significant mutational hotspot in ROS1.
PM6 No de novo observation has been reported for NM_002944.2:c.6079G>A.
PP1 No co-segregation data are available for NM_002944.2:c.6079G>A.
PP2 Missense constraint data for ROS1 are not available (HCI prior lookup returned 'gene_not_supported').
PP4 No patient phenotype data are available for this adjudication.
Benign
BA1 NM_002944.2:c.6079G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 NM_002944.2:c.6079G>A is absent from gnomAD.
BS2 No data are available on observation of NM_002944.2:c.6079G>A in healthy adult individuals.
BS3 No functional studies demonstrating a neutral or benign effect of p.Glu2027Lys have been identified.
BS4 No segregation data are available to demonstrate lack of co-segregation with disease.
BP1 Although ROS1 loss of function is supported as a disease mechanism per the PVS1 gene context literature review, the evidence does not establish that only truncating variants cause disease.
BP2 No evidence that NM_002944.2:c.6079G>A has been observed in trans with a known pathogenic variant in ROS1.
BP4 REVEL predicts a damaging score of 0.923, strongly inconsistent with a benign in silico profile.
BP5 No alternate molecular cause for the observed phenotype has been identified in a case carrying NM_002944.2:c.6079G>A.
BP6 ClinVar reports NM_002944.2:c.6079G>A as Uncertain Significance by a single submitter (Salgia Laboratory, City of Hope) with no assertion criteria provided.
N/A · 8 PVS1 · PS1 · PM3 · PM4 · PM5 · PP5 · BP3 · BP7
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