Starting
Initialising…
0%
SH2B3
Final classification
VUS
SH2B3 c.*2C>T · p.?
SH2B3

The SH2B3 c.*2C>T (NP_005466.1:p.?) variant has not been reported in ClinVar.

Gene
SH2B3
Transcript
NM_005475.2
HGVS · transcript:coding
NM_005475.2:c.*2C>T
Consequence
N/A
GRCh38
chr12:111448304 C>T
GRCh37
chr12:111886108 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 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
SH2B3 c.*2C>T

The SH2B3 c.*2C>T (NP_005466.1:p.?) variant has not been reported in ClinVar.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity below the usual PM2 threshold of 0.001 (0.1%).2 Although SH2B3 loss of function is an established disease mechanism, this variant is a 3'UTR substitution rather than a nonsense, frameshift, or canonical splice variant, so generic PVS1 criteria do not apply.3 In silico splice prediction does not support a splice-altering effect, with a SpliceAI maximum delta score of 0.04.4

PM2 VUS
3 pvs1_gene_contextpvs1_variant_assessmentpvs1_generic_framework ↗
Gene diagram · NM_005475.2 · variants mapped to exon structure
SH2B3 NM_005475.2
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 = 0.04).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      Sources & reference links
      5Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB