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SF3B1
Final classification
VUS
SF3B1 c.1873C>A · p.Arg625Ser
SF3B1

The variant c.1873C>A (p.Arg625Ser) in SF3B1 alters a residue in a statistically significant mutational hotspot, meeting PM1 at moderate strength.

Gene
SF3B1
Transcript
NM_012433.3
HGVS · transcript:coding
NM_012433.3:c.1873C>A
Consequence
N/A
GRCh38
chr2:197402760 G>T
GRCh37
chr2:198267484 G>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: PM1 moderate, PM2 moderate; combination = 2 moderate, 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: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
SF3B1 c.1873C>A

The variant c.1873C>A (p.Arg625Ser) in SF3B1 alters a residue in a statistically significant mutational hotspot, meeting PM1 at moderate strength. The variant is extremely rare in population databases, present at an allele frequency of 6.2e-07 (1/1,613,940 alleles) in gnomAD v4.1 and absent from gnomAD v2.1, meeting PM2 at moderate strength.1 Computational evidence is discordant: REVEL predicts a deleterious effect (0.806) but BayesDel predicts a benign effect (0.235), and SpliceAI predicts no splicing impact (delta 0.12). PP3 and BP4 are not met.2 No variant-specific publications, ClinVar classifications, de novo reports, functional studies, or segregation data are available. Multiple criteria (PS2, PS3, PS4, PM6, PP1, PP4, BS2, BS3, BS4, BP2, BP5) could not be assessed.3 The variant is absent from ClinVar and has not been classified by any germline reputable source; PP5 and BP6 are not met.4 Two moderate pathogenic criteria (PM1, PM2) are met with zero benign criteria met. This falls short of the Likely Pathogenic threshold (≥3 moderate, or ≥2 moderate + ≥2 supporting, or ≥1 strong + ≥1 moderate) per ACMG/AMP 2015 combination rules. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM1 + PM2 VUS
2 revelbayesdelspliceai ↗
5 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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 6.19602e-07; MAF= 0.00006%, 1/1613940 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09818e-05; MAF= 0.00110%, 1/91060 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 / 1,613,940
      0 hom
      South Asian
      1 / 91,060
      0.0011%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
      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 = 0.12). REVEL score = 0.806. BayesDel score = 0.235333.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      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 Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV59228873, n = 3 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots