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RB1
Final classification
VUS
RB1 c.743G>C · p.Gly248Ala
RB1

PM2 (moderate): The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, with an allele frequency of 0% in all queried population databases, supporting moderate evidence for pathogenicity.

Gene
RB1
Transcript
NM_000321.2
HGVS · transcript:coding
NM_000321.2:c.743G>C
Consequence
N/A
GRCh38
chr13:48362839 G>C
GRCh37
chr13:48936975 G>C
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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
RB1 c.743G>C

PM2 (moderate): The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, with an allele frequency of 0% in all queried population databases, supporting moderate evidence for pathogenicity.1 BP1 (supporting benign): RB1 is a gene in which >80% of pathogenic germline variants are truncating, and missense variants account for only 9.2% of pathogenic variants (PMID:42461076). This missense variant occurs in a gene where the primary disease mechanism is loss of function through null alleles. BP4 (supporting benign): Multiple lines of computational evidence — REVEL score 0.272, BayesDel score -0.129, and SpliceAI max delta 0.01 — converge on a non-deleterious prediction, providing supporting evidence against pathogenicity.2 Classification: Uncertain Significance (VUS). There is conflicting evidence: PM2 (moderate pathogenicity) from complete absence in population databases is offset by BP1 (supporting benign) and BP4 (supporting benign). The two supporting benign criteria do not reach the 'likely benign' threshold in the presence of a moderate pathogenic criterion. Additional evidence — particularly functional studies, segregation data, or clinical case reports — is needed to resolve this variant's clinical significance.

PM2 + BP4 VUS
Gene diagram · NM_000321.2 · variants mapped to exon structure
RB1 NM_000321.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with a population allele frequency of 0%. This meets the PM2 threshold for absence from large population databases (AF < 0.1% under non-VCEP generic ACMG rules).
gnomAD v2.1: absent (AF = 0). gnomAD v4.1: absent (AF = 0). gnomAD-Canada v1.0: absent (AF = 0). Complete absence across all queried population databases.
BP4 supporting Benign
Multiple lines of computational evidence suggest no deleterious effect. REVEL score is 0.272 (benign range, below 0.5 threshold). BayesDel score is -0.129 (negative, benign prediction). SpliceAI max delta score is 0.01 (no splicing impact, well below 0.2). Three independent in silico predictors concur on a benign or non-deleterious prediction, satisfying BP4 at supporting benign strength.
REVEL: 0.272 (benign). BayesDel: -0.129154 (benign). SpliceAI: max delta 0.01 (no splice impact). Three convergent benign predictions from independent computational methods.
Assessed · not applied
Pathogenic
PS1 No known pathogenic variant affecting the same amino acid (Gly248) via a different nucleotide change has been identified.
PS2 No de novo data available; both paternal and maternal confirmation were not assessed.
PS3 No variant-specific functional data available.
PS4 No case-control data or statistical enrichment data available for this variant in affected individuals versus controls.
PM1 Residue Gly248 is located in the N-terminal region of RB1, outside the well-characterized Pocket A and Pocket B domains.
PM6 No de novo data available for this variant.
PP1 No co-segregation data available.
PP2 RB1 is a tumor suppressor gene where truncating variants (nonsense, frameshift, splice-site, large deletions) account for >80% of pathogenic germline variants (PMID:42461076).
PP3 Multiple in silico predictors do not support a deleterious effect.
PP4 No patient phenotype or family history data are available.
PP5 This variant is absent from ClinVar.
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No observation data in healthy adult controls are available.
BS3 No well-established functional studies demonstrating no deleterious effect are available for this variant.
BS4 No segregation data available.
BP1 RB1 is a gene in which >80% of pathogenic germline variants are truncating (nonsense, frameshift, splice-site, large deletions).
BP2 No data on whether this variant has been observed in trans with a known pathogenic variant.
BP5 This variant is absent from ClinVar.
BP6 This variant is absent from ClinVar.
N/A · 3 PVS1 · PM5 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
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.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.272. BayesDel score = -0.129154.
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. 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 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