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SF3B1
Final classification
VUS
SF3B1 c.2352G>A · p.Met784Ile
SF3B1

NM_012433.3:c.2352G>A (p.Met784Ile) is a missense variant in SF3B1, a gene encoding a core spliceosome component associated with both somatic malignancy and constitutional neurodevelopmental disorders.

Gene
SF3B1
Transcript
NM_012433.3
HGVS · transcript:coding
NM_012433.3:c.2352G>A
Consequence
N/A
GRCh38
chr2:197401760 C>T
GRCh37
chr2:198266484 C>T
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
SF3B1 c.2352G>A

NM_012433.3:c.2352G>A (p.Met784Ile) is a missense variant in SF3B1, a gene encoding a core spliceosome component associated with both somatic malignancy and constitutional neurodevelopmental disorders. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (allele frequency = 0.0), meeting PM2 at moderate strength.1 Multiple in silico predictors suggest no significant impact: BayesDel score is 0.179 (benign range) and SpliceAI predicts no splicing alteration (max delta = 0.02), meeting BP4 at supporting benign strength. REVEL score of 0.538 is intermediate.2 The variant is absent from ClinVar and has not been reported in the published literature as a germline variant. COSMIC records one somatic occurrence (COSV106472208) without functional characterization.3 No variant-specific functional studies (PS3), de novo observations (PS2/PM6), co-segregation data (PP1), or case-control data (PS4) are available. Computational evidence is equivocal (PP3 not met). No pathogenic comparator at the same residue exists (PM5 not met). The variant does not lie in a statistically significant hotspot (cancerhotspots.org) and position 784 is not a recognized recurrent mutation site (PM1 not met). SF3B1 germline disease involves both missense and loss-of-function variants (PMID:41577671), so BP1 does not apply. With one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is insufficient for classification. The variant remains a Variant of Uncertain Significance (VUS) under ACMG/AMP 2015 generic rules.4

PM2 + BP4 VUS
2 bayesdelspliceai ↗revel
4 generic_acmg_combination_rules
Gene diagram · NM_012433.3 · variants mapped to exon structure
SF3B1 NM_012433.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada population databases (allele frequency = 0.0). Under generic ACMG/AMP 2015, absence from large population cohorts meets PM2 at moderate strength for a dominant disorder with AF well below 0.1%.
Absent from gnomAD v2.1 (0 alleles). Absent from gnomAD v4.1 (0 alleles). Absent from gnomAD-Canada v1.0 (0 alleles). Allele frequency 0.0well below the 0.1% PM2 threshold.
BP4 supporting Benign
Multiple lines of computational evidence suggest no significant impact on the gene product. BayesDel predicts a benign score of 0.179 (below the damaging threshold of ~0.27). SpliceAI predicts no splicing alteration (max delta score = 0.02). REVEL score of 0.538 is intermediate and does not overturn the two concordant benign/neutral predictions.
BayesDel: 0.179 (benign). SpliceAI max delta: 0.02 (no splicing impact). REVEL: 0.538 (intermediate). Two of three in silico predictors support no damaging effect.
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at codon 784 producing the same amino acid change (p.Met784Ile) has been established as pathogenic.
PS2 No de novo testing data with confirmed paternity and maternity is available for this variant.
PS3 No variant-specific functional studies have been performed for NM_012433.3:c.2352G>A (p.Met784Ile).
PS4 No case-control or cohort prevalence data are available to assess enrichment of this variant in affected individuals compared to controls.
PM1 The variant (p.Met784Ile) does not lie within a statistically significant mutational hotspot per cancerhotspots.org, and position 784 is not a recognized recurrent somatic mutation site in SF3B1.
PM5 No pathogenic missense variant at the same amino acid residue (Met784) has been identified.
PM6 No de novo observation data are available for this variant.
PP1 No family co-segregation data are available for this variant.
PP2 HCI prior constraint data are not available for SF3B1; the gene is not in the HCI prior database.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No patient phenotype or clinical data are available to assess whether the presentation is highly specific for SF3B1-related disease.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency = 0.0).
BS1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency = 0.0).
BS2 The variant has not been observed in any healthy individuals in population databases.
BS3 No well-established functional studies demonstrating no deleterious effect are available for this variant.
BS4 No family segregation data demonstrating non-segregation with disease are available.
BP1 SF3B1 germline disease is associated with both missense and loss-of-function variants.
BP2 No data on observation of this variant in trans with a known pathogenic dominant variant are available.
BP5 No data are available to determine whether an alternative molecular basis for disease has been identified in a case carrying this variant.
BP6 The variant is absent from ClinVar; no reputable source has classified this variant as benign or likely benign.
N/A · 6 PVS1 · PM3 · PM4 · PP5 · BP3 · 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 = 0.02). REVEL score = 0.538. BayesDel score = 0.179088.
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. SF3B1, a component of the spliceosome complex, is frequently mutated in hematologic malignancies.
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 previously been reported in somatic cancers (COSMIC; COSV106472208, n = 1 times).
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