Starting
Initialising…
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RECQL4
Final classification
Likely Pathogenic
RECQL4 c.2296del · p.Arg766GlyfsTer77
RECQL4

The RECQL4 c.2296del (p.Arg766GlyfsTer77) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as Benign by 3 single-submitter clinical laboratory submissions.

Gene
RECQL4
Transcript
NM_004260.4
HGVS · transcript:coding
NM_004260.4:c.2296del
Consequence
N/A
GRCh38
chr8:144513384 CG>C
GRCh37
chr8:145738767 CGG>C
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: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
RECQL4 c.2296del

The RECQL4 c.2296del (p.Arg766GlyfsTer77) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as Benign by 3 single-submitter clinical laboratory submissions.1 This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, supporting rarity for a RECQL4 germline variant.2 This deletion causes a frameshift with premature termination, and the generic PVS1 framework supports loss-of-function interpretation because RECQL4 loss of function is an established germline disease mechanism.3 SpliceAI predicts no significant splice impact for this variant with a maximum delta score of 0.15, and missense-oriented predictors such as REVEL and BayesDel are not applicable to this deletion.4

PVS1 + PM2 Likely Pathogenic
Gene diagram · NM_004260.4 · variants mapped to exon structure
RECQL4 NM_004260.4
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.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      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.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (3 clinical laboratories). (ClinVarID = 1327943)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.15).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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
      Triaged references · 8 PMIDs not cited in assessment
      12734318 ↗ Association between osteosarcoma and deleterious mutations in the RECQL4 gene in Rothmund-Thomson syndrome. ONCOKB
      15897384 ↗ A patient with Rothmund-Thomson syndrome and all features of RAPADILINO. ONCOKB
      18716613 ↗ The mutation spectrum in RECQL4 diseases. ONCOKB
      23842644 ↗ DNA helicases involved in DNA repair and their roles in cancer. ONCOKB
      28481359 ↗ Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. ONCOKB
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      20301383 ↗ Baller-Gerold Syndrome. CLINVAR
      20301415 ↗ Rothmund-Thomson Syndrome. CLINVAR