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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 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
The variant alters residue Arg625, which lies in a statistically significant mutational hotspot in SF3B1. SF3B1 hotspot mutations cluster in the HEAT domain, and codon 625 is a well-established recurrent mutation site.
CancerHotspots: residue R625 is in a statistically significant mutational hotspot (residue_significant: true).
PM2 moderate Pathogenic
This variant is extremely rare in population databases. It is absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 6.2e-07 (1/1,613,940 alleles, 0 homozygotes), with the single observation in the South Asian subpopulation (AF 1.1e-05). This frequency is well below the 0.1% PM2 threshold for non-VCEP assessment.
gnomAD v4.1: AF 6.2e-07 (1/1613940 alleles
Assessed · not applied
Pathogenic
PS2 No de novo reports with confirmed maternity and paternity are available for this variant.
PS3 No variant-specific well-established functional studies are available.
PS4 No case-control or variant prevalence data in affected versus unaffected individuals are available.
PM6 No de novo reports (confirmed or unconfirmed parentage) are available for this variant.
PP1 No co-segregation data in affected families is available for this variant.
PP2 SF3B1 is a gene where missense variants are a known disease mechanism (germline de novo missense variants cause neurodevelopmental disorders per PMID:41577671).
PP3 Multiple lines of computational evidence do not consistently support a deleterious effect.
PP4 No patient phenotype or clinical data are available for this variant.
PP5 This variant is absent from ClinVar and has not been classified by any reputable source.
Benign
BA1 The allele frequency of this variant in gnomAD v4.1 is 6.2e-07 (0.000062%), which is far below the 1% BA1 threshold.
BS1 The allele frequency of this variant in gnomAD v4.1 is 6.2e-07 (0.000062%), which is far below the 0.3% BS1 threshold for non-VCEP assessment.
BS2 No data on observation of this variant in healthy adult controls are available.
BS3 No variant-specific well-established functional studies demonstrating a benign effect are available.
BS4 No family segregation data are available to evaluate lack of segregation with disease.
BP2 No data on observation of this variant in trans with a pathogenic variant are available.
BP4 Multiple lines of computational evidence do not consistently suggest no impact on the gene product.
BP5 No data are available on cases harboring this variant with an alternate molecular basis for disease.
BP6 This variant is absent from ClinVar; no reputable source has reported it as benign.
N/A · 8 PVS1 · PS1 · PM3 · PM4 · PM5 · BP1 · BP3 · BP7
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