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SLX4
Final classification
Likely Benign
SLX4 c.903G>C · p.Lys301Asn
SLX4

NM_032444.3:c.903G>C (p.Lys301Asn) is a missense variant in SLX4, a Fanconi anemia gene (FANCP) where biallelic loss-of-function variants are the established disease mechanism. As a missense change, PVS1 is not applicable.

Gene
SLX4
Transcript
NM_032444.3
HGVS · transcript:coding
NM_032444.3:c.903G>C
Consequence
N/A
GRCh38
chr16:3602165 C>G
GRCh37
chr16:3652166 C>G
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, BP1 supporting benign, BP4 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
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, BP1 supporting benign, BP4 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP1BP4 Likely Benign
SLX4 c.903G>C

NM_032444.3:c.903G>C (p.Lys301Asn) is a missense variant in SLX4, a Fanconi anemia gene (FANCP) where biallelic loss-of-function variants are the established disease mechanism. As a missense change, PVS1 is not applicable.1 The variant is present at extremely low frequency in population databases: gnomAD v2.1 (1/31,392 alleles, AF 0.0032%) and gnomAD v4.1 (1/1,614,028 alleles, AF 0.00006%), meeting PM2 at supporting level for rarity below the 0.1% threshold.2 Multiple in silico predictors consistently support a benign effect: REVEL 0.148 (benign), BayesDel -0.375 (neutral), and SpliceAI max delta 0.01 (no splicing impact), meeting BP4 at supporting benign level.3 SLX4 is a gene where primarily truncating variants cause Fanconi anemia (FANCP); as a missense variant in a gene where the primary pathogenic mechanism is loss of function, BP1 applies at supporting benign level.4 The variant is absent from ClinVar and has not been reported as pathogenic by any reputable source. No variant-specific functional studies, case-control data, segregation data, or de novo observations are available.5 The evidence is limited and conflicting: one supporting pathogenic criterion (PM2) and two supporting benign criteria (BP1, BP4). Under ACMG/AMP 2015 rules, the variant is classified as a Variant of Uncertain Significance (VUS).6

PM2 + BP1 + BP4 Likely Benign
1 pvs1_gene_contextpvs1_variant_assessment
3 revelbayesdelspliceai ↗
4 pvs1_gene_context
6 generic_acmg_combination_rules
Gene diagram · NM_032444.3 · variants mapped to exon structure
SLX4 NM_032444.3
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 · supports benign
      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= 6.19568e-07; MAF= 0.00006%, 1/1614028 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47432e-07; MAF= 0.00008%, 1/1180036 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.18552e-05; MAF= 0.00319%, 1/31392 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.4834e-05; MAF= 0.00648%, 1/15424 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,614,028
      0 hom
      European (non-Finnish)
      1 / 1,180,036
      8.5e-05%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0032% · 1 / 31,392
      0 hom
      European (non-Finnish)
      1 / 15,424
      0.0065%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, 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 = 0.01). REVEL score = 0.148. BayesDel score = -0.374959.
      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. SLX4, a protein involved in DNA damage repair, is mutated in the germline of the FANCP subtype of Fanconi anemia patients.
      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; COSV107310564, n = 1 times).
      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