Variant classification summary

NM_002944.2:c.6609C>A

ROS1 · NP_002935.2:p.(Asp2203Glu) · NM_002944.2

GRCh37: chr6:117622261 G>T · GRCh38: chr6:117301098 G>T

Gene: ROS1 Transcript: NM_002944.2

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

ROS1

Transcript

NM_002944.2

Protein

NP_002935.2:p.(Asp2203Glu)

gnomAD AF

2.4985851761440084e-06 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

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.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_002944.2:c.6609C>A is a missense variant (p.Asp2203Glu). It does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants; PVS1 is not applicable to this variant class.	pvs1_variant_assessment pvs1_generic_framework
PS1	N/A	No prior pathogenic or likely pathogenic classification exists for a different nucleotide change at c.6609 producing the same amino acid substitution (p.Asp2203Glu).	clinvar
PS2	N/A	No de novo data available for this variant.
PS3	Not met	No well-established in vitro or in vivo functional studies support a damaging effect on the gene or gene product. OncoKB classifies this variant as Unknown Oncogenic Effect with no variant-specific functional evidence. No publications mention this variant.	oncokb
PS4	Not met	No case-control or cohort data support enrichment of this variant in affected individuals. The variant is absent from ClinVar with no clinical assertions.	clinvar gnomad_v4
PS5	N/A	No evidence applicable; PS5 is not assessed.
PM1	Not met	This variant does not lie in a statistically significant mutational hotspot (cancerhotspots.org). The p.Asp2203Glu substitution is a conservative amino acid change (both acidic residues) located in the C-terminal region of ROS1 (exon 43 of 43), distal to the tyrosine kinase domain core. No evidence supports this residue as a critical functional domain with absence of benign variation.
PM2	Met	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 gnomad_v4 gnomad_canada
PM5	N/A	No pathogenic or likely pathogenic missense comparator identified at residue Asp2203. The automated PM5 candidate harvest confirmed zero same-residue candidates in ClinVar.	pm5_candidates
PM6	N/A	No de novo data available for this variant.
PP1	N/A	No co-segregation data available for this variant.
PP2	N/A	While ROS1 has emerging literature-based support for germline disease (familial lung cancer risk, hereditary breast cancer), the gene-level constraint metrics are unavailable (HCI prior not found) and the germline disease mechanism is not sufficiently established to apply PP2 in the generic ACMG/AMP framework.
PP3	Not met	Multiple in silico prediction tools uniformly predict a benign effect. REVEL score is 0.14 (well below 0.5 threshold), BayesDel score is −0.455671 (negative = predicted benign), and SpliceAI delta score is 0.01 (no predicted splice impact). No computational tool supports a deleterious effect.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or clinical data are available for this variant. Absent from ClinVar with no clinical assertions.	clinvar
PP5	N/A	No evidence applicable; PP5 is not assessed.
BA1	Not met	Allele frequency in gnomAD v4.1 is 0.00025% (2.50×10⁻⁶), well below the 1% BA1 threshold. This variant is not a common polymorphism.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	Allele frequency in gnomAD v4.1 is 0.00025% (2.50×10⁻⁶), below the 0.3% BS1 threshold. The variant is not observed at a frequency greater than expected for the disorder.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	N/A	No data available on observation of this variant in healthy adult controls for a fully penetrant disorder.
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrate no damaging effect on protein function or splicing. While computational tools predict a benign effect, this alone is insufficient to meet BS3 without experimental functional data.
BS4	N/A	No co-segregation data available to demonstrate lack of segregation with disease.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. ROS1 has literature-based support for LOF as a germline disease mechanism (PMID:41390056, PMID:32906649), so the premise of BP1 is not met — truncating variants are not the sole established disease mechanism.	pvs1_gene_context
BP2	N/A	No data available on observation in trans with a pathogenic variant.
BP3	N/A	Skipped per instruction: variant type is substitution, not in-frame indel in a repetitive region.
BP4	Met	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 bayesdel spliceai
BP5	N/A	No evidence applicable; BP5 is not assessed.
BP6	N/A	No evidence applicable; BP6 is not assessed.
BP7	N/A	NM_002944.2:c.6609C>A is a missense variant (p.Asp2203Glu), not a synonymous variant. BP7 (synonymous variant with no predicted splice impact) does not apply.

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