Classification rationale

PVS1PM2 Likely Pathogenic

RB1 c.345_351del

NM_000321.2:c.345_351del is a frameshift deletion in exon 3 of RB1 predicted to produce a premature stop codon (p.Phe115LeufsTer8) and trigger nonsense-mediated decay, meeting PVS1 at very strong strength.¹ This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (0 alleles across >1.8 million total alleles), meeting PM2 at moderate strength.² No benign or conflicting evidence was identified. The variant is absent from ClinVar and has not been reported in any published literature with variant-specific data.³ Combined classification: PVS1 (very strong) + PM2 (moderate) → Pathogenic under generic ACMG/AMP 2015 combination rules (PMID:25741868).⁴

PVS1 + PM2 → Likely Pathogenic

1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment

2 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

3 clinvar ↗

4 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 · 16 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

✓

PVS1 very strong Pathogenic

NM_000321.2:c.345_351del is a 7bp frameshift deletion in exon 3 of RB1, predicted to produce a premature stop codon at position 122 (p.Phe115LeufsTer8), triggering nonsense-mediated decay. RB1 loss-of-function is a well-established disease mechanism for retinoblastoma, and this null variant meets PVS1 at full (very strong) strength under the generic ClinGen SVI PVS1 framework (PMC6185798).

Frameshift deletion c.345_351del introduces premature termination at codon 122 in exon 3 of 27well upstream of the last exon and predicted to undergo NMDRB1 germline loss-of-function is a confirmed disease mechanism for retinoblastoma

pvs1_generic_framework ↗

✓

PM2 moderate Pathogenic

NM_000321.2:c.345_351del is absent from all population databases: gnomAD v2.1 (0/~251,496 alleles), gnomAD v4.1 (0/~1,614,324 alleles), and gnomAD-Canada v1.0 (0 observed). This complete absence in large, diverse control populations meets PM2 at moderate strength under generic ACMG/AMP rules.

Absent from gnomAD v2.1 (exomesn~125748)

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

Assessed · not applied · 16 not met · 0 not assessed

Pathogenic

PS2 No de novo data are available for this variant.

PS3 No well-established functional studies of NM_000321.2:c.345_351del were identified.

PS4 No case-control or prevalence data are available.

PM1 The variant c.345_351del lies in exon 3 (N-terminal region, codon 115), outside the well-characterized RB1 pocket domain (codons ~380–785).

PM6 No de novo data are available for this variant.

PP1 No segregation data are available for this variant.

PP4 No patient phenotype or family history data are provided in the case.

PP5 No reputable source has classified this variant as pathogenic.

Benign

BA1 BA1 requires an allele frequency >1% in population databases.

BS1 BS1 requires an allele frequency greater than expected for the disorder (>0.3% per the adopted threshold).

BS2 BS2 requires observation in healthy adults with full penetrance expected, or observation in trans with a pathogenic variant.

BS3 No well-established functional studies demonstrate a benign or neutral effect for this variant.

BS4 No segregation data are available to demonstrate lack of segregation with disease.

BP2 BP2 requires observation in trans with a dominant pathogenic variant or in cis with a pathogenic variant in any inheritance pattern.

BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.

BP6 BP6 requires a reputable source to report the variant as benign.

N/A · 9 PS1 · PM4 · PM5 · PP2 · PP3 · BP1 · BP3 · BP4 · BP7

Research & evidence

Population frequency · supports pathogenic

gnomAD v4.1

gnomAD v2.1

v4.1

Absent from gnomAD v4.1.

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

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

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.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant is absent from ClinVar.

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).

SpliceAI ↗

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

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.

COSMIC ↗ Hotspots ↗

Sources & reference links

8Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 5 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

Re-run this variant?