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SRSF2
Final classification
VUS
SRSF2 c.283C>A · p.Pro95Thr
SRSF2

PM1 (moderate): Pro95 is located within the RRM domain of SRSF2, a well-established functional domain and mutational hotspot where other pathogenic missense changes (P95H, P95L, P95R) have been documented in COSMIC. Cancer Hotspots confirms the residue as statistically significant.

Gene
SRSF2
Transcript
NM_003016.4
HGVS · transcript:coding
NM_003016.4:c.283C>A
Consequence
N/A
GRCh38
chr17:76736878 G>T
GRCh37
chr17:74732960 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 supporting, BP4 supporting; combination = 1 moderate + 1 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
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 supporting, BP4 supporting; combination = 1 moderate + 1 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
Classification rationale
PM1PM2 BP4 VUS
SRSF2 c.283C>A

PM1 (moderate): Pro95 is located within the RRM domain of SRSF2, a well-established functional domain and mutational hotspot where other pathogenic missense changes (P95H, P95L, P95R) have been documented in COSMIC. Cancer Hotspots confirms the residue as statistically significant.1 PM2 (supporting): This variant is present at extremely low frequency in gnomAD (v2.1: 2/239,628 alleles, AF=8.35e-06; v4.1: 11/1,611,376 alleles, AF=6.83e-06), well below the 0.1% PM2 threshold. No homozygotes observed. Absent from gnomAD-Canada.2 BP4 (supporting): Multiple lines of computational evidence suggest no significant impact: REVEL score 0.444, BayesDel score -0.15213 (benign), and SpliceAI max delta score 0.00 (no predicted splicing effect).3 Overall assessment: 1 moderate pathogenic criterion (PM1) + 1 supporting pathogenic criterion (PM2) + 1 supporting benign criterion (BP4). Using generic ACMG/AMP 2015 combination rules (PMID:25741868), this combination of criteria is insufficient to reach Likely Pathogenic (requires ≥2 moderate or 1 moderate + ≥4 supporting), Likely Benign (requires ≥1 strong benign + 1 supporting benign, or ≥2 supporting benign), or Benign. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM1 + PM2 + BP4 VUS
3 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_003016.4 · variants mapped to exon structure
SRSF2 NM_003016.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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= 6.82646e-06; MAF= 0.00068%, 11/1611376 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09878e-05; MAF= 0.00110%, 1/91010 alleles, homozygotes = 0); grpmax FAF= 4.29e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 8.34627e-06; MAF= 0.00083%, 2/239628 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.87716e-05; MAF= 0.00188%, 2/106544 alleles, homozygotes = 0); grpmax FAF= 3.12e-06.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00068% · 11 / 1,611,376
      0 hom · FAF 0.00043%
      South Asian
      1 / 91,010
      0.0011%
      European (non-Finnish)
      10 / 1,179,354
      0.00085%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.00083% · 2 / 239,628
      0 hom · FAF 0.00031%
      European (non-Finnish)
      2 / 106,544
      0.0019%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      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 = 0.00). REVEL score = 0.444. BayesDel score = -0.15213.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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; COSV57970203, n = 11 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots