Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
EZHIP
Final classification
VUS
EZHIP c.860_892del · p.Gly287_Pro297del
EZHIP

NM_203407.3:c.860_892del (p.Gly287_Pro297del) is an in-frame deletion of 11 amino acids within exon 1 of EZHIP, a gene for which loss-of-function is a supported germline disease mechanism.

Gene
EZHIP
Transcript
NM_203407.3
HGVS · transcript:coding
NM_203407.3:c.860_892del
Consequence
N/A
GRCh38
chrX:51407860 TGCGATTCTGCGCCAGGCCCTGCCCGCCGAGGCC>T
GRCh37
chrX:51150712 TGCGATTCTGCGCCAGGCCCTGCCCGCCGAGGCC>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, PM4 moderate; combination = 1 moderate + 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, PM4 moderate; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PM4 VUS
EZHIP c.860_892del

NM_203407.3:c.860_892del (p.Gly287_Pro297del) is an in-frame deletion of 11 amino acids within exon 1 of EZHIP, a gene for which loss-of-function is a supported germline disease mechanism.1 This variant is extremely rare in population databases, with an allele frequency of 0.00135% in gnomAD v2.1 (2/147,648 alleles) and 0.00239% in gnomAD v4.1 (13/544,257 alleles), meeting PM2 at supporting strength.2 As an in-frame deletion in a non-repeat region, the variant meets PM4 at moderate strength per generic ACMG/AMP criteria.3 PVS1 is not applicable as this in-frame deletion does not fall into the null-variant buckets (nonsense, frameshift, or canonical splice) defined by the ClinGen SVI PVS1 framework.4 No computational evidence supports pathogenicity (SpliceAI max delta = 0.04; REVEL/BayesDel not applicable to deletions), so PP3 is not met.5 The variant is absent from ClinVar, and no functional studies, cosegregation data, or de novo reports were identified. Multiple criteria (PS2, PS3, PS4, PS5, PM6, PP1, PP4, BS2, BS3, BS4, BP2, BP5) remain unassessed due to lack of evidence.6

PM2 + PM4 VUS
Gene diagram · NM_203407.3 · variants mapped to exon structure
EZHIP NM_203407.3
Fetching transcript structure from UCSC…
Applied criteria · 2 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= 2.38858e-05; MAF= 0.00239%, 13/544257 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.99483e-05; MAF= 0.00399%, 12/300388 alleles, homozygotes = 0); grpmax FAF= 2.228e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.35457e-05; MAF= 0.00135%, 2/147648 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 8.30496e-05; MAF= 0.00830%, 1/12041 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0024% · 13 / 544,257
      0 hom · FAF 0.0022%
      European (non-Finnish)
      12 / 300,388
      0.004%
      East Asian
      1 / 29,804
      0.0034%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0014% · 2 / 147,648
      0 hom
      East Asian
      1 / 12,041
      0.0083%
      European (non-Finnish)
      1 / 62,387
      0.0016%
      + 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, 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 = 0.04).
      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