NM_000321.2:c.2341C>T

RB1 · NP_000312.2:p.(Pro781Ser) · NM_000321.2

GRCh37: chr13:49039356 C>T · GRCh38: chr13:48465220 C>T

Gene: RB1 Transcript: NM_000321.2

Final call

VUS

PM2 moderate

Variant details

Gene

RB1

Transcript

NM_000321.2

Protein

NP_000312.2:p.(Pro781Ser)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

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).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	N/A	This is a missense variant (c.2341C>T, p.Pro781Ser); it does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework
PS1	Not met	No evidence that the same amino acid change (Pro781Ser) has been previously established as pathogenic in an independent source. The variant is absent from ClinVar and no literature reports were identified linking this exact change to pathogenicity.	clinvar
PS2	Not met	No de novo occurrence data (with confirmed maternity and paternity) was identified for this variant.
PS3	Not met	No variant-specific functional data is available. OncoKB reports unknown oncogenic effect with no reviewed functional evidence. COSMIC reports a single somatic occurrence but without functional characterization. No literature reports with experimental functional data for this exact variant or a systematically characterized range encompassing Pro781 were identified.	oncokb
PS4	Not met	No case-control or cohort data demonstrating statistically increased prevalence of this variant in affected individuals versus controls.
PS5	N/A	PS5 is not a standard ACMG/AMP 2015 criterion. No evidence framework defines applicability for this code in the generic ACMG context.
PM1	Not met	Position 781 (Pro781Ser) is in the RB1 C-terminal domain, not within a statistically significant mutational hotspot as defined by cancerhotspots.org. While the C-terminal domain is functionally relevant, no domain-level hotspot or critical functional motif specifically encompassing residue 781 is characterized in the available evidence to satisfy PM1.
PM2	Met	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).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No same-residue comparator missense variants with an established pathogenic classification were identified. The automated PM5 candidate search returned zero eligible candidates at residue 781.	pm5_candidates
PM6	Not met	No de novo occurrence was reported for this variant (without confirmation of paternity and maternity).
PP1	Not met	No co-segregation data in affected family members is available for this variant.
PP2	Not met	RB1 has both pathogenic and benign missense variants; it is not a gene with a low rate of benign missense variation. A large integrative study (PMID:42461076) reports that missense variants account for 9.2% of germline RB1 variants, indicating that missense variation is observed. Without evidence that benign missense variation is rare in RB1, PP2 does not apply.
PP3	Not met	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). Multiple lines of computational evidence do not agree on a deleterious effect, so PP3 is not met.	revel bayesdel spliceai
PP4	Not met	No phenotype data is available for the proband(s) carrying this variant. The patient's clinical presentation relative to RB1-associated disease (retinoblastoma/osteosarcoma) cannot be assessed.
PP5	Not met	This variant is absent from ClinVar. No reputable source (expert panel, clinical laboratory) has classified this variant as pathogenic.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, well below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all population databases. Allele frequency of 0% does not exceed the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No data is available demonstrating this variant has been observed in healthy adults. Absence from gnomAD is insufficient to confirm observation in healthy individuals for a dominant disorder.
BS3	Not met	No functional studies demonstrating a benign effect for this variant are available. OncoKB reports unknown oncogenic effect with no reviewed functional evidence.	oncokb
BS4	Not met	No segregation data demonstrating lack of co-segregation with disease is available.
BP1	Not assessed	This is a missense variant in RB1, a gene for which truncating variants are the primary known disease mechanism. A large integrative analysis (PMID:42461076) reports that truncating germline variants account for >80% of pathogenic RB1 variants, while missense variants comprise only 9.2%. BP1 applies at supporting benign strength.
BP2	Not met	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	Not met	In silico predictions are conflicting. REVEL scores 0.728 (damaging), which precludes BP4. Multiple lines of computational evidence do not agree on a benign or neutral effect.	revel bayesdel spliceai
BP5	Not met	No data is available demonstrating this variant is found in a case with an alternate molecular basis for disease.
BP6	Not met	This variant is absent from ClinVar. No reputable source has classified it as benign or likely benign.	clinvar
BP7	N/A	This is a missense variant (c.2341C>T, p.Pro781Ser), not a synonymous or intronic variant. BP7 does not apply.

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