Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
RB1
Final classification
VUS
RB1 c.2236G>T · p.Glu746Ter
RB1

NM_000321.2:c.2236G>T (p.Glu746Ter) is a nonsense variant in exon 22 of RB1, introducing a premature termination codon predicted to trigger nonsense-mediated decay in a gene with an established loss-of-function disease mechanism for retinoblastoma.

Gene
RB1
Transcript
NM_000321.2
HGVS · transcript:coding
NM_000321.2:c.2236G>T
Consequence
N/A
GRCh38
chr13:48465022 G>T
GRCh37
chr13:49039158 G>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: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 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: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
RB1 c.2236G>T

NM_000321.2:c.2236G>T (p.Glu746Ter) is a nonsense variant in exon 22 of RB1, introducing a premature termination codon predicted to trigger nonsense-mediated decay in a gene with an established loss-of-function disease mechanism for retinoblastoma.1 PVS1 is met at very strong strength.2 This variant is extremely rare in population databases, absent from gnomAD v2.1 and observed in only 1 of 1,187,988 alleles in gnomAD v4.1 (AF = 8.42e-7), satisfying PM2 at supporting strength.3 This variant has been reported in ClinVar as Pathogenic by two clinical laboratories (Variation ID 1069507, 2-star review status) and is listed in association with retinoblastoma.4 This variant has been observed in the somatic context in COSMIC (COSV57314725, n = 6), consistent with a pathogenic role, though somatic data alone do not independently satisfy germline ACMG criteria. No variant-specific functional studies, de novo observations, co-segregation data, or statistical case-frequency data were identified in the reviewed literature to satisfy PS3, PS2, PS4, or PP1. Under the generic ACMG/AMP 2015 combination rules (PMID:25741868), one very strong criterion (PVS1) plus one supporting criterion (PM2) does not reach the threshold for Likely Pathogenic or Pathogenic classification. The combination of PVS1 and PM2 alone results in a variant of uncertain significance (VUS) by strict scoring.5 Note: In clinical practice, a PVS1-level nonsense variant in RB1 with ClinVar Pathogenic consensus and extreme population rarity would typically be classified as at least Likely Pathogenic. The strict ACMG/AMP 2015 scoring framework requires additional supporting criteria to reach Likely Pathogenic (e.g., 1 Very Strong + 1 Moderate, or 1 Strong + 2 Supporting). ClinVar submissions from two clinical laboratories and somatic COSMIC observations provide orthogonal clinical support not captured by the generic scoring matrix.6

PVS1 + PM2 VUS
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
5 generic_acmg_combination_rules
6 clinvar ↗generic_acmg_combination_rules
Gene diagram · NM_000321.2 · variants mapped to exon structure
RB1 NM_000321.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
Nonsense variant NM_000321.2:c.2236G>T (p.Glu746Ter) in exon 22 of 27 introduces a premature termination codon at position 746 of 929 amino acids, predicted to trigger nonsense-mediated decay. RB1 has an established loss-of-function disease mechanism for retinoblastoma. Under the ClinGen SVI PVS1 framework (PMC6185798), this nonsense variant qualifies for PVS1 at very strong strength.
Nonsense substitution producing premature termination codon at p.Glu746TerRB1 loss of function is an established germline disease mechanism for retinoblastomaVariant is in exon 22 of 27
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 and is extremely rare in gnomAD v4.1 (1/1,187,988 alleles; AF 8.42e-7), well below the 0.1% threshold for PM2. The single observation is in the East Asian subpopulation (AF 3.84e-5).
gnomAD v2.1: absent (0 alleles)gnomAD v4.1: 1/1187
Assessed · not applied
Pathogenic
PS1 No data available on whether an alternative nucleotide change at c.2236 (e.g., c.2236G>A producing the same p.Glu746Ter) has been established as pathogenic.
PS2 No confirmed de novo observation of NM_000321.2:c.2236G>T was identified in the literature reviewed.
PS3 No variant-specific functional data was identified for NM_000321.2:c.2236G>T (p.Glu746Ter).
PS4 The variant has been reported in ClinVar as Pathogenic by two clinical laboratories, and one submission notes a bilateral retinoblastoma case, but no systematic case-control or case-frequency data are available to establish statistically significant enrichment in affected individuals.
PM1 Residue Glu746 is located in the C-terminal region of RB1, but this position is not within a statistically significant mutational hotspot (cancerhotspots.org negative).
PM5 This variant produces a premature termination codon (p.Glu746Ter), not a missense change.
PM6 No confirmed de novo observation of NM_000321.2:c.2236G>T with confirmed maternity and paternity was identified in the available literature.
PP1 No co-segregation data for NM_000321.2:c.2236G>T in affected families was identified in the available literature.
PP4 No detailed patient phenotype data specific to NM_000321.2:c.2236G>T is available to assess whether the clinical presentation is highly specific for RB1-related disease.
PP5 ClinVar reports this variant as Pathogenic (2 clinical laboratories, 2-star review status: criteria provided, multiple submitters, no conflicts).
Benign
BA1 The maximum population allele frequency for this variant is 3.84e-5 (East Asian, gnomAD v4.1), which is far below the BA1 threshold of 1%.
BS1 The maximum population allele frequency is 3.84e-5, well below the BS1 threshold of 0.3%.
BS2 No homozygous observations of this variant are reported in gnomAD or any other population database.
BS3 No functional studies demonstrating a benign effect for NM_000321.2:c.2236G>T (p.Glu746Ter) were identified.
BS4 No segregation data are available to assess lack of co-segregation with disease.
BP2 No data are available indicating that this variant has been observed in trans with a known pathogenic RB1 variant in a healthy individual.
BP5 This variant is not reported as benign in ClinVar or any other reputable database.
BP6 ClinVar reports this variant as Pathogenic, not Benign or Likely Benign.
N/A · 8 PM3 · PM4 · PP2 · PP3 · BP1 · BP3 · BP4 · 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= 8.41759e-07; MAF= 0.00008%, 1/1187988 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 3.83907e-05; MAF= 0.00384%, 1/26048 alleles, homozygotes = 0).
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
8.4e-05% · 1 / 1,187,988
0 hom
East Asian
1 / 26,048
0.0038%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
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 Pathogenic (2 clinical laboratories). (ClinVarID = 1069507)
SpliceAI screenshot
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.27). BayesDel score = 0.66.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
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; COSV57314725, n = 6 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
Triaged references · 8 PMIDs not cited in assessment
14769601 ↗ Rapid identification of germline mutations in retinoblastoma by protein truncation testing. ONCOKB
22205104 ↗ RB1 mutations and second primary malignancies after hereditary retinoblastoma. ONCOKB
26607597 ↗ Deletion of Rb1 induces both hyperproliferation and cell death in murine germinal center B cells. ONCOKB
30206110 ↗ The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial. ONCOKB
31138663 ↗ RB1 Deletion in Retinoblastoma Protein Pathway-Disrupted Cells Results in DNA Damage and Cancer Progression. ONCOKB
12173465 ↗ [Spectrum and frequencies of RB1 gene structural defects in retinoblastoma]. CLINVAR
17096365 ↗ Genotype-phenotype correlations in hereditary familial retinoblastoma. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR