Variant classification summary

NM_000321.2:c.345_351delCACTTTT

RB1 · NP_000312.2:p.(Phe115LeufsTer8) · NM_000321.2

GRCh37: chr13:48916812 GTTCACTT>G · GRCh38: chr13:48342676 GTTCACTT>G

Gene: RB1 Transcript: NM_000321.2

Final call

Likely Pathogenic

PVS1 very strong PM2 moderate

Variant details

Gene

RB1

Transcript

NM_000321.2

Protein

NP_000312.2:p.(Phe115LeufsTer8)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

Combined classification: PVS1 (very strong) + PM2 (moderate) → Pathogenic under generic ACMG/AMP 2015 combination rules (PMID:25741868).

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	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).	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment
PS1	N/A	PS1 applies to a nucleotide change producing the same amino acid change as an established pathogenic missense variant. This is a 7bp frameshift deletion — no same-amino-acid comparator concept applies.
PS2	Not met	No de novo data are available for this variant. Neither ClinVar submissions nor published literature provide de novo confirmation.
PS3	Not met	No well-established functional studies of NM_000321.2:c.345_351del were identified. OncoKB classifies this variant as 'Likely Oncogenic' based on somatic/oncogenicity curation, which does not constitute independent germline functional evidence for PS3.	oncokb
PS4	Not met	No case-control or prevalence data are available. The variant is absent from ClinVar and has not been reported in affected individuals through published studies or databases.	clinvar
PS5	N/A	PS5 requires a reputable source to have recently reported the variant as pathogenic with evidence unavailable for independent evaluation. No ClinVar entry or other reputable source classifies this variant.
PM1	Not met	The variant c.345_351del lies in exon 3 (N-terminal region, codon 115), outside the well-characterized RB1 pocket domain (codons ~380–785). No statistically significant hotspot encompasses this position, and the Cancer Hotspots database does not list this variant or residue as a significant hotspot.
PM2	Met	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.	gnomad_v2 gnomad_v4 gnomad_canada
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants causing protein length changes. This is an out-of-frame frameshift deletion producing a premature termination codon, assessed under PVS1.
PM5	N/A	PM5 requires a novel missense change at a residue where a different pathogenic missense change has been established. This is a frameshift deletion, not a missense variant; classic same-residue PM5 semantics cannot be applied.	pm5_candidates
PM6	Not met	No de novo data are available for this variant. PM6 requires a confirmed de novo observation with maternity and paternity confirmation.
PP1	Not met	No segregation data are available for this variant. No family studies or cosegregation analyses have been reported in ClinVar or published literature.
PP2	N/A	PP2 assesses the rate of benign missense variation in the gene. This is a frameshift deletion, not a missense variant.
PP3	N/A	PP3 evaluates multiple lines of computational evidence for deleterious effect. For a frameshift null variant predicted to undergo NMD, the deleterious effect is inherent to the variant type and already captured by PVS1. SpliceAI shows no significant splice impact (max delta score 0.02), and REVEL/BayesDel are unavailable (not a SNV). Applying PP3 alongside PVS1 for this null variant would constitute double-counting.	spliceai
PP4	Not met	No patient phenotype or family history data are provided in the case. PP4 requires that the patient's phenotype is highly specific for a disease with a single genetic etiology and that this has been confirmed in the case.
PP5	Not met	No reputable source has classified this variant as pathogenic. The variant is absent from ClinVar, and OncoKB's 'Likely Oncogenic' classification is a somatic oncogenicity label, not an ACMG/AMP germline assertion.	clinvar oncokb
BA1	Not met	BA1 requires an allele frequency >1% in population databases. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	BS1 requires an allele frequency greater than expected for the disorder (>0.3% per the adopted threshold). The variant is absent from all population databases.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	BS2 requires observation in healthy adults with full penetrance expected, or observation in trans with a pathogenic variant. The variant is absent from population databases; no observation in healthy individuals is available.
BS3	Not met	No well-established functional studies demonstrate a benign or neutral effect for this variant. No functional evidence suggesting normal protein function was identified.
BS4	Not met	No segregation data are available to demonstrate lack of segregation with disease. No family studies have been reported for this variant.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. This is a frameshift truncating variant, not a missense variant.
BP2	Not met	BP2 requires observation in trans with a dominant pathogenic variant or in cis with a pathogenic variant in any inheritance pattern. No such data are available for this variant.
BP3	N/A	BP3 applies to in-frame deletions or insertions in repetitive regions. This is an out-of-frame frameshift deletion, not an in-frame variant.
BP4	N/A	BP4 evaluates computational evidence suggesting no impact on the gene product. For a frameshift null variant predicted to cause NMD and complete loss of protein function, the concept of 'no impact' is inapplicable. The SpliceAI max delta score of 0.02 addresses splicing only and does not override the established null effect of the frameshift.	spliceai
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such clinical context is available for this variant.
BP6	Not met	BP6 requires a reputable source to report the variant as benign. The variant is absent from ClinVar and no source classifies it as benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. This is a frameshift deletion, not a synonymous variant.

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