Classification rationale

PM2 VUS

RB1 c.2341C>T

PM2 is met at moderate strength: the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada in a gene where pathogenic variants are expected to be rare.¹ BP1 is met at supporting benign strength: this is a missense variant in RB1, a gene where truncating variants are the primary disease mechanism (>80% of pathogenic variants are truncating per PMID:42461076). Under the generic ACMG/AMP 2015 combination rules (PMID:25741868), one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP1) do not combine to reach any classification threshold. The variant is classified as a Variant of Uncertain Significance (VUS).²

PM2 → VUS

1 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

2 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 · 1 applied · 22 assessed

Applied · 1

Strength Supporting Moderate Strong Very strong

✓

PM2 moderate Pathogenic

This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0 (genomes), supporting moderate evidence for pathogenicity under the generic ACMG/AMP framework (allele frequency <0.1% in large population cohorts for a dominant disorder).

Absent from gnomAD v2.1 (AF = nullno observations).Absent from gnomAD v4.1 (AF = null

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

Assessed · not applied

Pathogenic

PS1 No evidence that the same amino acid change (Pro781Ser) has been previously established as pathogenic in an independent source.

PS2 No de novo occurrence data (with confirmed maternity and paternity) was identified for this variant.

PS3 No variant-specific functional data is available.

PS4 No case-control or cohort data demonstrating statistically increased prevalence of this variant in affected individuals versus controls.

PM1 Position 781 (Pro781Ser) is in the RB1 C-terminal domain, not within a statistically significant mutational hotspot as defined by cancerhotspots.org.

PM5 No same-residue comparator missense variants with an established pathogenic classification were identified.

PM6 No de novo occurrence was reported for this variant (without confirmation of paternity and maternity).

PP1 No co-segregation data in affected family members is available for this variant.

PP2 RB1 has both pathogenic and benign missense variants; it is not a gene with a low rate of benign missense variation.

PP3 In silico predictions are conflicting: REVEL scores 0.728 (damaging), but BayesDel scores -0.0665 (neutral/benign) and SpliceAI shows no splicing impact (max delta 0.01).

PP4 No phenotype data is available for the proband(s) carrying this variant.

PP5 This variant is absent from ClinVar.

Benign

BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.

BS1 The variant is absent from all population databases.

BS2 No data is available demonstrating this variant has been observed in healthy adults.

BS3 No functional studies demonstrating a benign effect for this variant are available.

BS4 No segregation data demonstrating lack of co-segregation with disease is available.

BP1 This is a missense variant in RB1, a gene for which truncating variants are the primary known disease mechanism.

BP2 No data is available showing this variant is observed in trans with a known pathogenic RB1 variant, which would support benign classification for a dominant disorder.

BP4 In silico predictions are conflicting.

BP5 No data is available demonstrating this variant is found in a case with an alternate molecular basis for disease.

BP6 This variant is absent from ClinVar.

N/A · 2 PVS1 · BP7

Research & evidence

Population frequency

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 = 0.01). REVEL score = 0.728. BayesDel score = -0.0665026.

SpliceAI ↗

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. RB1, a regulator of the cell cycle, is inactivated by mutation, deletion or allelic loss in various cancer types, including retinoblastoma and lung ca

OncoKB ↗

COSMIC

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; COSV108030570, n = 1 times).

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