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ZRSR2
Final classification
VUS
ZRSR2 c.617T>C · p.Phe206Ser
ZRSR2

The ZRSR2 c.617T>C (p.Phe206Ser; p.F206S) variant has not been reported in ClinVar and does not lie in a statistically significant hotspot.

Gene
ZRSR2
Transcript
NM_005089.3
HGVS · transcript:coding
NM_005089.3:c.617T>C
Consequence
N/A
GRCh38
chrX:15815736 T>C
GRCh37
chrX:15833859 T>C
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 supporting; combination = 1 supporting, 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 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
ZRSR2 c.617T>C

The ZRSR2 c.617T>C (p.Phe206Ser; p.F206S) variant has not been reported in ClinVar and does not lie in a statistically significant hotspot.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, corresponding to an observed population frequency of 0%, which is below the 0.1% PM2 threshold.2 Available curated review did not identify variant-specific reviewed functional evidence for this variant.3 In silico evidence is mixed: BayesDel is positive at 0.563308, while SpliceAI predicts no significant splice impact with a maximum delta score of 0.09, so computational findings do not currently support PP3 or BP4.4

PM2 VUS
Gene diagram · NM_005089.3 · variants mapped to exon structure
ZRSR2 NM_005089.3
Fetching transcript structure from UCSC…
Applied criteria · 1 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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      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.
      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 = 0.09). BayesDel score = 0.563308.
      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. ZRSR2, a splicing factor, is altered in various hematological 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 not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots