Starting
Initialising…
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DDX41
Final classification
Likely Pathogenic
DDX41 c.1480_1496dup · p.Ala500ArgfsTer52
DDX41

NM_016222.2:c.1480_1496dup is a frameshifting duplication predicted to produce p.(Ala500ArgfsTer52) [p.(A500Rfs*52)], altering the reading frame from codon 500 and truncating the normal C-terminal portion of DDX41; this is consistent with a loss-of-function effect in a gene for which loss of function has been implicated in DDX41-related hematologic malignancy predisposition syndrome.

Gene
DDX41
Transcript
NM_016222.2
HGVS · transcript:coding
NM_016222.2:c.1480_1496dup
Consequence
N/A
GRCh38
chr5:177512548 A>AGGGAAGTCCAGGCCCTT
GRCh37
chr5:176939549 A>AGGGAAGTCCAGGCCCTT
Basis ACMG/AMP qualitative combination: PVS1_Strong + PM2_Supporting
ACMG/AMP qualitative combination: PVS1_Strong + PM2_Supporting
Classification rationale
PVS1PM2 Likely Pathogenic
DDX41 c.1480_1496dup

NM_016222.2:c.1480_1496dup is a frameshifting duplication predicted to produce p.(Ala500ArgfsTer52) [p.(A500Rfs*52)], altering the reading frame from codon 500 and truncating the normal C-terminal portion of DDX41; this is consistent with a loss-of-function effect in a gene for which loss of function has been implicated in DDX41-related hematologic malignancy predisposition syndrome.1 The variant is absent from gnomAD v2.1 and is seen once in gnomAD v4.1 at AF 6.84053e-07 (1/1,461,874 alleles), with highest observed population AF 8.99276e-07 in non-Finnish Europeans, supporting marked rarity in population databases.2 Because the predicted premature termination occurs in the terminal exon, the available loss-of-function evidence is most appropriately weighted below full very-strong strength, and no additional independently curated case-level or functional evidence in the supplied materials upgrades the variant beyond the likely pathogenic range. Overall, the available evidence supports classification of NM_016222.2:c.1480_1496dup (DDX41 p.(Ala500ArgfsTer52)) as Likely Pathogenic.3

PVS1 + PM2 Likely Pathogenic
Gene diagram · NM_016222.2 · variants mapped to exon structure
DDX41 NM_016222.2
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
      This variant is present in gnomAD v4.1 (AF= 6.84053e-07; MAF= 0.00007%, 1/1461874 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.99276e-07; MAF= 0.00009%, 1/1112006 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.8e-05% · 1 / 1,461,874
      0 hom
      European (non-Finnish)
      1 / 1,112,006
      9e-05%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Middle Eastern, South Asian, Ashkenazi Jewish, East Asian, African/African American)
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (2 clinical laboratories).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
      Functional / OncoKB screenshot
      Functional
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      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.
      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 PMID:26712909
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PVS1 supports · met
      PMID PMID:36322930
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PVS1 supports · met
      Sources & reference links
      6Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB