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
      v4.1
      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).
      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).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00018% · 1 / 563,095
      0 hom
      European (non-Finnish)
      1 / 305,623
      0.00033%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      Absent · 0 / 162,702
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-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 = 0.01). 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.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID 31548708
      Found
      Residue 206 falls within the PRC2-binding domain (residues 200–391) a critical functional domain Multiple pathogenic/de novo missense variants reported in this domain (PMID:31548708 PMID:32325000)
      Applied to
      PM1 supports · met
      PMID 32325000
      Found
      Residue 206 falls within the PRC2-binding domain (residues 200–391) a critical functional domain Multiple pathogenic/de novo missense variants reported in this domain (PMID:31548708 PMID:32325000)
      Applied to
      PM1 supports · met
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots