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ASXL1
Final classification
Likely Pathogenic
ASXL1 c.2822del · p.Pro941LeufsTer4
ASXL1

The ASXL1 c.2822del (p.(Pro941LeufsTer4)) variant has been observed in somatic cancers and is absent from ClinVar.

Gene
ASXL1
Transcript
NM_015338.5
HGVS · transcript:coding
NM_015338.5:c.2822del
Consequence
N/A
GRCh38
chr20:32435532 GC>G
GRCh37
chr20:31023335 GC>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback.
Classification rationale
PVS1PM2 Likely Pathogenic
ASXL1 c.2822del

The ASXL1 c.2822del (p.(Pro941LeufsTer4)) variant has been observed in somatic cancers and is absent from ClinVar.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 and supports rarity in the general population.2 Published studies and OncoKB support damaging loss-of-function biology for ASXL1 truncating variants, but available data do not provide a validated germline functional assay for this specific variant.3 This single-base deletion causes a frameshift predicted to truncate the protein after four altered amino acids, removing 598 of 1542 residues (38.8%), and SpliceAI predicts no significant additional splice effect with a maximum delta score of 0.02.4

PVS1 + PM2 Likely Pathogenic
Gene diagram · NM_015338.5 · variants mapped to exon structure
ASXL1 NM_015338.5
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 · supports pathogenic
      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 = 0.02).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      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 previously been reported in somatic cancers (COSMIC; COSV60115810, n = 2 times).
      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