Starting
Initialising…
0%
EZHIP
Final classification
VUS
EZHIP c.616G>A · p.Ala206Thr
EZHIP

NM_203407.3:c.616G>A (p.Ala206Thr) in EZHIP is absent from ClinVar.

Gene
EZHIP
Transcript
NM_203407.3
HGVS · transcript:coding
NM_203407.3:c.616G>A
Consequence
N/A
GRCh38
chrX:51407632 G>A
GRCh37
chrX:51150484 G>A
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 supporting, PM2 supporting, BP4 supporting benign; combination = 2 supporting + 1 supporting benign, 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 supporting, PM2 supporting, BP4 supporting benign; combination = 2 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM1PM2 BP4 VUS
EZHIP c.616G>A

NM_203407.3:c.616G>A (p.Ala206Thr) in EZHIP is absent from ClinVar.1 The variant is extremely rare in population databases, absent from gnomAD v2.1 (0/162,702 alleles) and present as a singleton in gnomAD v4.1 (1/563,095 alleles, AF=0.000178%), meeting PM2 at supporting strength.2 p.Ala206Thr lies within the PRC2-binding domain of EZHIP (residues 200–391), a well-characterized functional domain where pathogenic missense variants cluster, meeting PM1 at supporting strength. SpliceAI predicts no splicing impact (max delta=0.01) and BayesDel yields a benign-leaning score of −0.673766, meeting BP4 at supporting benign strength.3 No functional studies, de novo observations, co-segregation data, or case-control evidence are available for this variant. No reputable source classification exists.4 With two supporting pathogenic criteria (PM1_supporting, PM2_supporting) and one supporting benign criterion (BP4_supporting_benign), the evidence is insufficient to classify the variant as pathogenic or benign. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM1 + PM2 + BP4 VUS
3 spliceai ↗bayesdel
5 generic_acmg_combination_rules
Gene diagram · NM_203407.3 · variants mapped to exon structure
EZHIP NM_203407.3
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
      Population frequency
      Overall AF
      1 / 563,095
      0.00018%
      Highest · European (non-Finnish)
      0.00033%
      Homozygotes
      0
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 1 / 305,623 0.00033% 0
      Admixed American 0 / 44,589
      European (Finnish) 0 / 45,836
      Amish 0 / 686
      East Asian 0 / 30,409
      Middle Eastern 0 / 3,239
      South Asian 0 / 43,442
      Ashkenazi Jewish 0 / 17,901
      African/African American 0 / 45,160
      This variant is present in gnomAD v4.1 (AF= 1.7759e-06; MAF= 0.00018%, 1/563095 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.27201e-06; MAF= 0.00033%, 1/305623 alleles, homozygotes = 0).
      Overall AF
      Not observed
      Homozygotes
      0
      Not observed in any ancestry group across 8 populations in gnomAD v2.1.
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/162702 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/11612 alleles, homozygotes = 0).
      Absent from gnomAD-Canada v1.0.
      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 = 0.01). BayesDel score = -0.673766.
      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. EZHIP, a polycomb binding protein, is recurrently altered by rearrangement and mutation in endometrial stromal sarcomas and posterior fossa ependymoma
      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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots