0%
RB1c.2236G>TUncertain significance
Print report
Variant interpretation report

RB1 c.2236G>T, p.(Glu746Ter)

NM_000321.2:c.2236G>T NP_000312.2:p.(Glu746Ter) View identifiers
Classification
Uncertain significance

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About RB1

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 2 Benign evidence criteria: 0
Pathogenic criteria applied · 2
PVS1Very strong
PVS1 · very strong

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.

PM2Supporting
PM2 · supporting

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).

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

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.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

SpliceAI score
0.270 maximum delta

Recorded SpliceAI maximum delta score: 0.270. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
ClinVar submissions
2 reported laboratory submissions

2 Pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
6 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV57314725, n = 6 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

Context only
COSMIC ↗Cancer Hotspots ↗
For specialists

Technical detail

ACMG/AMP criteria under Not recorded, with the data and sources behind each one.

29 criteria with recorded statuses: 2 met · 17 not met · 1 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM3PM4PM5PM6PP1PP2PP3PP4PP5PS5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

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.

PVS1 is met at very strong strength.

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.

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.

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.

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.

Met · 2

PVS1 Very strongNonsense 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. Details ▾Hide ▴
Evidence considered
  • Nonsense substitution producing premature termination codon at p.Glu746Ter
  • RB1 loss of function is an established germline disease mechanism for retinoblastoma
  • Variant is in exon 22 of 27
  • NMD is expected
  • Variant is not in the last exon or a region known to escape NMD
Sources
pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
PM2 SupportingThis 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). Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: absent (0 alleles)
  • gnomAD v4.1: 1/1
  • 187
  • 988 alleles
  • AF = 8.42e-7
  • 0 homozygotes
  • gnomAD-Canada v1.0: absent
Sources
gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

Not met · 17 · evaluated, threshold not reached

PS2 No confirmed de novo observation of NM_000321.2:c.2236G>T was identified in the literature reviewed. PS2 requires a specific de novo report with confirmed maternity and paternity. Details ▾Hide ▴
Still missing
  • No de novo observation of this variant found in available literature
PS3 No variant-specific functional data was identified for NM_000321.2:c.2236G>T (p.Glu746Ter). The OncoKB-curated literature describes RB1 loss-of-function mechanisms at the gene level (protein truncation testing, RB1 deletion in cell lines, resistance studies) but none directly tested this specific variant or systematically characterized the region spanning codon 746. Details ▾Hide ▴
Still missing
  • No variant-specific functional assay data for 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. Details ▾Hide ▴
Evidence considered
  • ClinVar: 2 clinical laboratories classify as Pathogenic
  • One ClinVar submission reports at least 1 bilateral retinoblastoma case
Still missing
  • No systematic case-frequency or case-control data to satisfy PS4 statistical threshold
Sources
clinvar ↗
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). No evidence from the available literature characterizes codon 746 as lying within a well-defined critical functional domain meeting PM1 criteria. Details ▾Hide ▴
Evidence considered
  • cancerhotspots.org: no significant hotspot at RB1 E746
Still missing
  • No domain-level functional characterization of codon 746 in available evidence
PM5 This variant produces a premature termination codon (p.Glu746Ter), not a missense change. Automated PM5 candidate harvesting was unable to identify same-residue pathogenic missense comparator variants for this nonsense substitution. Details ▾Hide ▴
Evidence considered
  • pm5_candidates: no same-residue comparator variants found
Still missing
  • PM5 candidate search yielded no comparators for this nonsense variant
Sources
pm5_candidates
PM6 No confirmed de novo observation of NM_000321.2:c.2236G>T with confirmed maternity and paternity was identified in the available literature. Details ▾Hide ▴
Still missing
  • No de novo report with confirmed parentage found
PP1 No co-segregation data for NM_000321.2:c.2236G>T in affected families was identified in the available literature. One ClinVar submission notes a bilateral case and pedigree but without co-segregation details across multiple affected family members. Details ▾Hide ▴
Evidence considered
  • ClinVar SCV005046288: single bilateral retinoblastoma case noted
  • insufficient for PP1 co-segregation threshold
Still missing
  • No multi-generational segregation data available
Sources
clinvar ↗
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. The variant is reported in ClinVar in association with retinoblastoma, but detailed phenotypic data are not available. Details ▾Hide ▴
Evidence considered
  • ClinVar lists retinoblastoma as an associated condition
Still missing
  • No patient-level phenotypic detail available beyond condition association
Sources
clinvar ↗
PP5 ClinVar reports this variant as Pathogenic (2 clinical laboratories, 2-star review status: criteria provided, multiple submitters, no conflicts). The PP5 rule in effect requires a 3-star expert panel review for application at supporting strength. With 2 stars, PP5 is not met under the governing evidence policy. Details ▾Hide ▴
Evidence considered
  • ClinVar variation ID 1069507: Pathogenic
  • 2 submitters
  • 2-star review status
  • Review status: criteria provided
  • multiple submitters
  • no conflicts
Still missing
  • No 3-star expert panel review in ClinVar
Sources
clinvar ↗
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%. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 maximum subpopulation AF = 3.84e-5 (EAS)
  • well below 1%
Sources
gnomad_v4 ↗
BS1 The maximum population allele frequency is 3.84e-5, well below the BS1 threshold of 0.3%. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 max AF = 3.84e-5
  • far below 0.3%
Sources
gnomad_v4 ↗
BS2 No homozygous observations of this variant are reported in gnomAD or any other population database. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: 0 homozygotes
  • gnomAD v4.1: 0 homozygotes
Sources
gnomad_v2 ↗gnomad_v4 ↗
BS3 No functional studies demonstrating a benign effect for NM_000321.2:c.2236G>T (p.Glu746Ter) were identified. The available literature describes RB1 loss-of-function as a disease mechanism, which is consistent with a deleterious effect of this nonsense variant. Details ▾Hide ▴

No further detail was recorded.

BS4 No segregation data are available to assess lack of co-segregation with disease. Details ▾Hide ▴
Still missing
  • No segregation data available
BP2 No data are available indicating that this variant has been observed in trans with a known pathogenic RB1 variant in a healthy individual. Details ▾Hide ▴
Still missing
  • No data on observation in trans with known pathogenic variants
BP5 This variant is not reported as benign in ClinVar or any other reputable database. It is reported as Pathogenic by two clinical laboratories. Details ▾Hide ▴
Evidence considered
  • ClinVar: Pathogenic classification
  • no benign assertions
Sources
clinvar ↗
BP6 ClinVar reports this variant as Pathogenic, not Benign or Likely Benign. BP6 does not apply. Details ▾Hide ▴
Evidence considered
  • ClinVar classification is Pathogenic
  • not benign
Sources
clinvar ↗

Not assessed · 1 · no assessment recorded

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. Without this comparator, PS1 cannot be assessed. Details ▾Hide ▴
Still missing
  • No data on alternative nucleotide changes at c.2236 producing the same premature stop
Not applicable · 9· recorded as not applicable Show reasons ▾Hide reasons ▴
PM3 N/ASkipped per directive: trivially not_applicable. Details ▾Hide ▴

No further detail was recorded.

PM4 N/ASkipped per directive: trivially not_applicable. Details ▾Hide ▴

No further detail was recorded.

PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation where missense is a common disease mechanism. NM_000321.2:c.2236G>T is a nonsense variant, not a missense variant. Details ▾Hide ▴

No further detail was recorded.

PP3 N/AFor nonsense variants where PVS1 is applied at very strong strength, PP3 (in silico prediction of deleterious effect) is not independently applied. The predicted protein truncation effect is already captured by PVS1. SpliceAI max delta score of 0.27 does not add independent evidence. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.27 (DS_DL = 0.27
  • DS_AL = 0.15)
  • BayesDel score = 0.66
Sources
spliceai ↗bayesdel
BP1 N/ABP1 applies to missense variants in genes where truncating variants are the primary disease mechanism. This is a nonsense (truncating) variant, not a missense variant. Details ▾Hide ▴

No further detail was recorded.

BP3 N/ASkipped per directive: trivially not_applicable. Details ▾Hide ▴

No further detail was recorded.

BP4 N/ABP4 applies when multiple lines of in silico evidence suggest no impact. For a nonsense variant with PVS1 applied, in silico predictors are not independently assessed for benign effect. Details ▾Hide ▴

No further detail was recorded.

BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. NM_000321.2:c.2236G>T is a nonsense variant, not a synonymous variant. Details ▾Hide ▴

No further detail was recorded.

PS5 N/APS5 applies to a novel missense variant at a codon where a different missense change is established as pathogenic. This is a nonsense variant, not a missense variant. Details ▾Hide ▴

No further detail was recorded.

Identifiers

Gene
RB1
Transcript
NM_000321.2
Coding (HGVS c.)
NM_000321.2:c.2236G>T
Protein (HGVS p.)
NP_000312.2:p.(Glu746Ter)
GRCh38
chr13:48465022 G>T
GRCh37
chr13:49039158 G>T
ClinVar
1069507
COSMIC
COSV57314725

Gene diagram

Every interpreted variant in RB1, mapped onto the exon structure of NM_000321.2. Select a row to find it on the plot.

RB1NM_000321.2
Fetching transcript structure from UCSC…
gnomAD v4.1 1 / 1,187,988 alleles AF 8.42e-07 · 0 homozygotes
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 8.4e-07 · 1 / 1,187,988 alleles · 0 hom
East Asian1 / 26,048 3.8e-05
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish).

Statements

gnomAD 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).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -24 bp
0.150
SpliceAI acceptor gainat +25 bp
0.000
SpliceAI donor lossat +89 bp
0.270
SpliceAI donor gainat -24 bp
0.000
Pangolin splice lossmagnitude shown
-0.590
Pangolin splice gain
0.010

Other predictors

REVEL
Not available
BayesDel
0.660

How the predictions were used

PP3 N/AFor nonsense variants where PVS1 is applied at very strong strength, PP3 (in silico prediction of deleterious effect) is not independently applied. The predicted protein truncation effect is already captured by PVS1. SpliceAI max delta score of 0.27 does not add independent evidence. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.27 (DS_DL = 0.27
  • DS_AL = 0.15)
  • BayesDel score = 0.66
Sources
spliceai ↗bayesdel
BP4 N/ABP4 applies when multiple lines of in silico evidence suggest no impact. For a nonsense variant with PVS1 applied, in silico predictors are not independently assessed for benign effect. Details ▾Hide ▴

No further detail was recorded.

BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. NM_000321.2:c.2236G>T is a nonsense variant, not a synonymous variant. Details ▾Hide ▴

No further detail was recorded.

Statement

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.27). BayesDel score = 0.66.

8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

  • Rapid identification of germline mutations in retinoblastoma by protein truncation testing.
    Describes protein truncation testing (PTT) methodology for rapid germline RB1 mutation detection in retinoblastoma. Reports detection of truncating mutations (nonsense, frameshift, splice site) in 19 of 27 probands. NM_000321.2:c.2236G>T was not specifically identified in this publication.
    Does not name this variant
    PMID 14769601 ↗
  • RB1 mutations and second primary malignancies after hereditary retinoblastoma.
    Retrospective cohort study of 199 hereditary retinoblastoma survivors examining RB1 genotype in relation to second primary malignancy risk. Analyzes RB1 mutation types (nonsense, frameshift, splice, missense) by domain. NM_000321.2:c.2236G>T was not specifically identified in this publication.
    Does not name this variant
    PMID 22205104 ↗
  • Deletion of Rb1 induces both hyperproliferation and cell death in murine germinal center B cells.
    Examines functional consequences of Rb1 deletion in murine germinal center B cells using conditional knockout models. Provides gene-level evidence for RB1 tumor suppressor function but does not test or mention NM_000321.2:c.2236G>T.
    Does not name this variant
    PMID 26607597 ↗
  • The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial.
    Reports circulating tumor DNA sequencing from PALOMA-3 trial identifying RB1 mutations as a resistance mechanism to CDK4/6 inhibition in breast cancer. Several RB1 mutations are described but NM_000321.2:c.2236G>T was not specifically identified.
    Does not name this variant
    PMID 30206110 ↗
  • RB1 Deletion in Retinoblastoma Protein Pathway-Disrupted Cells Results in DNA Damage and Cancer Progression.
    Investigates RB1 deletion in RB-pathway disrupted cancer cells using CRISPR/Cas9, demonstrating increased DNA damage and impaired homologous recombination repair. The study uses engineered RB1 deletions (exon 22 or exon 2) in U2OS, H460, and H1792 cell lines. NM_000321.2:c.2236G>T was not specifically tested or mentioned.
    Does not name this variant
    PMID 31138663 ↗
  • [Spectrum and frequencies of RB1 gene structural defects in retinoblastoma].
    Babenko OV et al. · 2002
    Russian-language study of RB1 structural defects in retinoblastoma using SSCP, heteroduplex analysis, and direct sequencing. Reports spectrum of mutations (nonsense, missense, splicing, frameshift) in tumor and blood samples. NM_000321.2:c.2236G>T was not specifically identified in the abstract-reviewed content.
    Does not name this variant
    PMID 12173465 ↗
  • Genotype-phenotype correlations in hereditary familial retinoblastoma.
    Taylor M et al. · 2007
    Reports genotype-phenotype correlations in 50 familial retinoblastoma pedigrees with 165 RB1 mutation carriers. Categorizes mutations by type and domain. NM_000321.2:c.2236G>T was not specifically identified in the abstract-reviewed content.
    Does not name this variant
    PMID 17096365 ↗
  • 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.
    ACMG/AMP standards and guidelines for sequence variant interpretation. Provides the classification framework and evidence criteria weighting rules used in this assessment. Does not discuss any specific variant.
    Does not name this variant
    PMID 25741868 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 1 / 1,187,988 recorded alleles Open source ↗
gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗
SpliceAI Lookup Recorded maximum delta 0.270 Open source ↗
ClinVar 2 Pathogenic Open source ↗
COSMIC Captured COSMIC source record Open source ↗
Cancer hotspots Captured Cancer Hotspots source record Open source ↗
OncoKB Captured OncoKB source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD 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).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Pathogenic (2 clinical laboratories). (ClinVarID = 1069507)

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.27). BayesDel score = 0.66.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57314725, n = 6 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.