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
ROS1
Final classification
VUS
PM2BP4
ROS1
c.6609C>A
p.Asp2203Glu
This variant
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-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
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 applied · 8 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
This variant is absent from gnomAD v2.1 and gnomAD-Canada, and is present in gnomAD v4.1 at an extremely low allele frequency (2.50×10⁻⁶; 4/1,600,906 alleles; 0 homozygotes; grpmax FAF=6.8×10⁻⁷), well below the 0.1% PM2 threshold for population-level absence. This low frequency in control populations provides supporting evidence for pathogenicity.
gnomAD v2.1: absentgnomAD v4.1: AF=2.50×10⁻⁶ (4/1600
✓
BP4
supporting
Benign
Multiple lines of computational evidence predict no impact on the gene product. REVEL score is 0.14 (benign-leaning), BayesDel score is −0.455671 (predicted benign), and SpliceAI predicts no splice alteration (max delta = 0.01). Additionally, the amino acid substitution is conservative (Asp→Glu; both are acidic residues with similar biochemical properties), further supporting a neutral effect.
REVEL: 0.14 (lowbenign range)BayesDel: −0.455671 (predicted benign)
Assessed · not applied
· 8 not met · 0 not assessed
Pathogenic
PS3
No well-established in vitro or in vivo functional studies support a damaging effect on the gene or gene product.
PS4
No case-control or cohort data support enrichment of this variant in affected individuals.
PM1
This variant does not lie in a statistically significant mutational hotspot (cancerhotspots.org).
PP3
Multiple in silico prediction tools uniformly predict a benign effect.
PP4
No patient phenotype or clinical data are available for this variant.
Benign
BA1
Allele frequency in gnomAD v4.1 is 0.00025% (2.50×10⁻⁶), well below the 1% BA1 threshold.
BS1
Allele frequency in gnomAD v4.1 is 0.00025% (2.50×10⁻⁶), below the 0.3% BS1 threshold.
BS3
No well-established in vitro or in vivo functional studies demonstrate no damaging effect on protein function or splicing.
N/A · 16
PVS1 · PS1 · PS2 · PM5 · PM6 · PP1 · PP2 · PP5 · BS2 · BS4 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1
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%
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
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
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
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.
COSMIC
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