Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
ROS1
Final classification
VUS
ROS1 c.5825G>A · p.Arg1942Gln
ROS1

NM_002944.2:c.5825G>A (p.Arg1942Gln) is a missense variant in exon 37 of the ROS1 gene, encoding a receptor tyrosine kinase implicated in familial lung cancer and hereditary breast cancer.

Gene
ROS1
Transcript
NM_002944.2
HGVS · transcript:coding
NM_002944.2:c.5825G>A
Consequence
N/A
GRCh38
chr6:117319983 C>T
GRCh37
chr6:117641146 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.5825G>A

NM_002944.2:c.5825G>A (p.Arg1942Gln) is a missense variant in exon 37 of the ROS1 gene, encoding a receptor tyrosine kinase implicated in familial lung cancer and hereditary breast cancer.1 This variant is present at extremely low frequency in gnomAD v4.1 (AF=0.000081%, 13/1,613,226 alleles, 0 homozygotes) and is absent from gnomAD v2.1. The grpmax filtering allele frequency is 8.75e-06, well below the 0.1% threshold for PM2 at supporting strength.2 In silico predictors are predominantly deleterious: REVEL score 0.706 (pathogenic-leaning) and SpliceAI max delta 0.99 (predicts acceptor gain with potential splice-altering effect). PP3 is applied at supporting strength.3 The variant is absent from ClinVar and COSMIC. No variant-specific functional studies, de novo reports, segregation data, or case-control analyses are available in the case materials.4 PVS1 is not applicable as this is a missense variant. The variant does not lie at a canonical splice consensus position and falls outside the null-variant buckets defined by the ClinGen PVS1 framework (PMC6185798).5 Only two supporting-level criteria (PM2_Supporting, PP3) are met. Per the ACMG/AMP 2015 combination rules, two supporting criteria are insufficient to reach a Likely Pathogenic classification. The variant is classified as a Variant of Uncertain Significance (VUS).6

PM2 + PP3 VUS
1 pvs1_gene_context
3 revelspliceai ↗
5 pvs1_variant_assessmentpvs1_generic_framework ↗
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 · 16 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_002944.2:c.5825G>A is present at extremely low frequency in gnomAD v4.1 (overall AF=0.000081%, 13/1,613,226 alleles, 0 homozygotes; grpmax FAF=8.75e-06). It is absent from gnomAD v2.1. The allele frequency is well below the 0.1% PM2 threshold for generic ACMG application.
gnomAD v2.1: absentgnomAD v4.1: AF=8.06e-06 (13/1613
PP3 supporting Pathogenic
Multiple in silico predictors support a deleterious effect. REVEL score 0.706 is above the pathogenic threshold, and SpliceAI predicts a strong cryptic acceptor gain (delta=0.99) that may alter splicing. BayesDel score 0.137 is discordant (benign-leaning). Two independent computational lines (REVEL for missense impact; SpliceAI for splice-altering potential) support a deleterious effect, meeting the PP3 threshold at supporting strength.
REVEL: 0.706 (pathogenic-leaningabove 0.644 threshold)SpliceAI: max delta 0.99 (acceptor gain AG=0.99
Assessed · not applied
Pathogenic
PS2 No de novo data are available for NM_002944.2:c.5825G>A.
PS3 No variant-specific functional data are available for p.Arg1942Gln.
PS4 No case-control or affected-prevalence data are available to demonstrate enrichment of this variant in affected individuals.
PM1 p.Arg1942Gln does not lie in a statistically significant mutational hotspot per cancerhotspots.org.
PM6 No de novo data are available.
PP1 No segregation data are available for this variant.
PP2 Insufficient data to apply PP2.
PP4 No patient-specific phenotype or clinical data are available in the case.
Benign
BA1 The overall gnomAD v4.1 allele frequency is 0.000081% (8.06e-06), far below the 1% BA1 threshold.
BS1 The overall gnomAD v4.1 allele frequency is 0.000081%, below the 0.3% BS1 threshold.
BS2 No data on healthy adult carriers are available.
BS3 No functional studies demonstrating no deleterious effect of p.Arg1942Gln are available.
BS4 No segregation data demonstrating lack of cosegregation with disease are available.
BP1 BP1 applies when a missense variant occurs in a gene where only truncating variants cause disease.
BP2 No data on observation of this variant in trans with a known pathogenic variant are available.
BP4 Computational evidence is not uniformly benign.
N/A · 7 PVS1 · PS1 · PM5 · PP5 · BP5 · BP6 · BP7
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= 8.05839e-06; MAF= 0.00081%, 13/1613226 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 4.45812e-05; MAF= 0.00446%, 2/44862 alleles, homozygotes = 0); grpmax FAF= 8.75e-06.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00081% · 13 / 1,613,226
0 hom · FAF 0.00087%
East Asian
2 / 44,862
0.0045%
South Asian
3 / 91,056
0.0033%
Remaining individuals
1 / 62,436
0.0016%
European (non-Finnish)
7 / 1,179,590
0.00059%
+ 6 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish, African/African American)
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 possible splice impact for this variant (max delta score = 0.99). REVEL score = 0.706. BayesDel score = 0.137147.
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