Classification rationale

PM2 BP4 VUS

RB1 c.*1G>C unknown · exon 27

PM2 (Supporting): variant seen once in 1,609,556 gnomAD v4.1 alleles (AF 6.2e-07), far below the 0.1% rarity threshold. BP4 (Supporting): SpliceAI max delta 0.007, well below the <0.1 threshold, indicating no predicted splicing impact. Combination of one supporting pathogenic (PM2) and one supporting benign (BP4) criterion maps to VUS under generic ACMG/AMP 2015 rules.

PM2 + BP4 → VUS

Gene diagram · NM_000321.3 · variants mapped to exon structure

RB1 NM_000321.3

Fetching transcript structure from UCSC…

Applied criteria · 2 applied · 17 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

✓

PM2 supporting review Pathogenic

Met (supporting): absent from gnomAD v2.1 and seen once in 1,609,556 gnomAD v4.1 alleles (AF ~6.2e-07), far below the 0.1% rarity threshold.

Generic non-VCEP PM2 operating threshold: AF <0.1% supports PM2; the gnomAD v4.1 AF of 6.212893493609418e-07 is below this threshold.The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0, and the gnomAD v4.1 record shows zero homozygotes.Because this is a 3' UTR variant with no established clinical or functional disease mechanism in the case bundle, rarity is treated as population evidence only and not as evidence of pathogenicity by itself.

gnomad_v4 ↗gnomad_v2 ↗gnomad_canada ↗

✓

BP4 supporting Benign

Met (supporting): SpliceAI max delta 0.007, well below the <0.1 threshold, indicating no predicted splicing impact.

SpliceAI Lookup (source_registry key 'spliceai') scores: DS_AG=0.003, DS_AL=0.007, DS_DG=0.0, DS_DL=0.0, max_delta_score=0.007; evidence_sentence 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01)'.Generic fallback rule (generic_acmg_classification_rules.md, PMID:25741868 base framework, SVI-recommended SpliceAI thresholds also reflected in VCEP CSPECs such as ATM's per Walker et al. 2023): SpliceAI max delta < 0.1 -> BP4 supporting for non-missense variants; observed max delta (~0.007-0.01) clearly falls under this threshold.No RB1-specific VCEP PP3/BP4 lookup spreadsheet was available to pre-assign a code (vcep_materials.json: no cspec url available), so the generic calibration governs.

spliceai ↗

Assessed · not applied · 5 not met · 12 not assessed

Pathogenic

PS2 Not assessed: no de novo observation or parental testing results were available to establish the variant arose spontaneously.

PS3 Not assessed: no validated functional assay data (e.g., splicing reporter or mRNA stability studies) were available for this variant.

PS4 Not assessed: no affected case series or case-control enrichment data were available.

PM3 Not assessed: no data showed the variant in trans with a pathogenic allele, so recessive-disease phase could not be evaluated.

PM6 Not assessed: no unconfirmed de novo observation or parental genotypes were documented.

PP1 Not assessed: no familial segregation or co-segregation data were available.

PP3 Not met: SpliceAI predicts no splicing impact (max delta 0.007) versus the >0.2 threshold required for PP3.

PP4 Not assessed: no proband phenotype or phenotype-specific testing context was supplied.

PP5 Not met: no ClinVar expert-panel pathogenic assertion exists for this exact variant.

Benign

BA1 Not met: allele frequency 6.2e-07 (1/1,609,556) is far below the population frequency expected for a benign variant.

BS1 Not met: the observed allele frequency (6.2e-07) shows no excess incompatible with disease causality.

BS2 Not assessed: no evidence showed the single gnomAD carrier is a phenotyped healthy adult.

BS3 Not assessed: no functional assay data demonstrating normal activity were available.

BS4 Not assessed: no tested unaffected relatives or non-segregation data were documented.

BP2 Not assessed: no family observations, second pathogenic variant, or phase information were available.

BP5 Not assessed: no alternate molecular diagnosis or phenotype data were available to establish another cause.

BP6 Not met: no ClinVar expert-panel benign or likely benign assertion exists for this exact variant.

N/A · 9 PVS1 · PS1 · PM1 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7

Research & evidence

Population frequency

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 6.21289e-07; MAF= 0.00006%, 1/1609556 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.50117e-07; MAF= 0.00009%, 1/1176308 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

6.2e-05% · 1 / 1,609,556
0 hom

European (non-Finnish)

1 / 1,176,308

8.5e-05%

+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)

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).

SpliceAI ↗

Functional No data

No calibrated functional assay or RNA evidence was identified for this variant.

OncoKB ↗

Somatic evidence

COSMIC

This variant has not previously been reported in somatic cancers (COSMIC).

Hotspots

This variant does not lie in a statistically significant cancer hotspot.

Sources & reference links

6Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB