Variant classification summary

NM_000321.2:c.2546_2547delAT

RB1 · NP_000312.2:p.(Asn849ThrfsTer5) · NM_000321.2

GRCh37: chr13:49050861 AAT>A · GRCh38: chr13:48476725 AAT>A

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.(Asn849ThrfsTer5)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000321.2:c.2546_2547delAT is a frameshift deletion in exon 25 of RB1, introducing a premature termination codon (p.Asn849ThrfsTer5) predicted to undergo nonsense-mediated decay. RB1 loss of function is the established germline disease mechanism for retinoblastoma.

2

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, supporting rarity in the general population.

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.2546_2547delAT is a frameshift deletion in exon 25 of 27, introducing a premature termination codon (p.Asn849ThrfsTer5) predicted to undergo nonsense-mediated decay (>50 bp upstream of the last exon-exon junction). RB1 is a well-established tumor suppressor gene where loss of function is the known disease mechanism for retinoblastoma. Under ClinGen SVI PVS1 recommendations (PMC6185798), this null variant in a gene where LoF is a known mechanism merits PVS1 at full (very strong) weight.	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment
PS1	N/A	PS1 applies to missense variants where the same amino acid change is known to be pathogenic. This variant is a frameshift deletion; PS1 is not applicable.
PS2	Not assessed	De novo status was not assessed; no parental testing data or de novo report for this variant was identified.
PS3	Not assessed	No variant-specific functional studies were identified. Five OncoKB-curated papers were reviewed; none mentioned NM_000321.2:c.2546_2547delAT. Well-established functional evidence supporting a damaging effect is not available for this variant.
PS4	Not assessed	No case-control or prevalence data comparing affected individuals to controls were available for this variant.
PS5	Not assessed	This variant is absent from ClinVar; no reputable source has classified it as pathogenic.
PM1	Not met	The variant does not lie within a statistically significant mutational hotspot as assessed by Cancer Hotspots, and no domain-specific enrichment was identified.
PM2	Met	This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, consistent with a rare pathogenic variant.	gnomad_v2 gnomad_v4 gnomad_canada
PM4	N/A	PM4 applies to in-frame deletions/insertions and stop-loss variants. This variant is a frameshift deletion, which is assessed under PVS1, not PM4.
PM5	N/A	PM5 requires a different missense change at the same residue known to be pathogenic. This variant is a frameshift deletion; no single-residue missense comparator can be defined.
PM6	Not assessed	No de novo observation with unconfirmed parentage was identified for this variant.
PP1	Not assessed	No segregation data in affected family members were available for this variant.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation. This variant is a frameshift deletion.
PP3	N/A	PP3 evaluates computational evidence of deleterious effect for missense or splice-site variants. This is a frameshift deletion whose damaging mechanism (protein truncation via NMD) is captured by PVS1. SpliceAI predicts no splicing impact (max delta 0.04), and REVEL/BayesDel are not applicable to non-SNV variants.	spliceai
PP4	Not assessed	No patient phenotype or family history data specific to this variant were available for review.
PP5	Not assessed	This variant is absent from ClinVar; no reputable source has reported it as pathogenic.
BA1	Not met	BA1 requires an allele frequency >1% in population databases. This 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 >0.3% in population databases. This variant is absent from all gnomAD populations.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not assessed	No data on observation in healthy adults for a disorder with full penetrance expected at early age were available.
BS3	Not assessed	No variant-specific functional studies demonstrating no damaging effect were identified. Five OncoKB-curated papers were reviewed; none mentioned NM_000321.2:c.2546_2547delAT.
BS4	Not assessed	No non-segregation data in affected families were available for this variant.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the predominant disease mechanism. This variant is itself a truncating (frameshift) variant.
BP2	N/A	BP2 applies to variants observed in trans with a pathogenic variant in a recessive disorder. RB1-associated retinoblastoma follows autosomal dominant inheritance with high penetrance; BP2 is not applicable.
BP3	N/A	BP3 applies to in-frame deletions or insertions in repetitive regions without a known function. This variant is a frameshift deletion.
BP4	N/A	BP4 applies to missense or splice variants where multiple lines of computational evidence suggest no impact. This is a frameshift deletion whose damaging mechanism is protein truncation via NMD, not missense substitution or altered splicing. SpliceAI predicts no splicing impact (max delta 0.04), but this is not the relevant pathogenic mechanism for a frameshift variant.	spliceai
BP5	Not assessed	No alternate locus observation suggesting a different molecular basis for disease was identified.
BP6	Not assessed	This variant is absent from ClinVar; no reputable source has classified it as benign.
BP7	N/A	BP7 applies to silent (synonymous) variants with no predicted splicing impact. This variant is a frameshift deletion, not a synonymous substitution.
PM3	N/A	Skipped by examiner directive.

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