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CUX1
Final classification
Likely Benign
CUX1 c.2383C>G · p.Leu795Val
CUX1

NM_001202543.1:c.2383C>G (p.Leu795Val) in CUX1 is classified as Likely Benign based on ACMG/AMP 2015 criteria.

Gene
CUX1
Transcript
NM_001202543.1
HGVS · transcript:coding
NM_001202543.1:c.2383C>G
Consequence
N/A
GRCh38
chr7:102201647 C>G
GRCh37
chr7:101844927 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, BP4 supporting, BP6 supporting; 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, BP4 supporting, BP6 supporting; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP4BP6 Likely Benign
CUX1 c.2383C>G

NM_001202543.1:c.2383C>G (p.Leu795Val) in CUX1 is classified as Likely Benign based on ACMG/AMP 2015 criteria. The variant is present in gnomAD v4.1 at low frequency (AF=0.0167%, 270/1,613,476 alleles, 0 homozygotes), meeting PM2_supporting; however, the observation in 270 alleles warrants caution in this assignment.1 Multiple in silico predictors concordantly support a benign effect: REVEL score 0.067, BayesDel score -0.544, and SpliceAI max delta 0.00 (BP4_supporting).2 Two independent clinical testing laboratories (Ambry Genetics, CeGaT) have classified this variant as Likely Benign in ClinVar VCV2371264 (BP6_supporting).3 No case reports, functional studies, or variant-specific literature were identified for this variant. All ClinVar-associated PMIDs are unrelated policy/position statements about newborn screening. With 2 supporting benign criteria (BP4, BP6) versus 1 supporting pathogenic criterion (PM2), the benign evidence outweighs the pathogenic evidence, resulting in a Likely Benign classification per generic ACMG/AMP 2015 combination rules (PMID:25741868).4

PM2 + BP4 + BP6 Likely Benign
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_001202543.1 · variants mapped to exon structure
CUX1 NM_001202543.1
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= 0.000167341; MAF= 0.01673%, 270/1613476 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000222899; MAF= 0.02229%, 263/1179904 alleles, homozygotes = 0); grpmax FAF= 0.0002003.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.0006516780710329097, 12/18414 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.017% · 270 / 1,613,476
      0 hom · FAF 0.02%
      European (non-Finnish)
      263 / 1,179,904
      0.022%
      Admixed American
      3 / 60,010
      0.005%
      Remaining individuals
      3 / 62,460
      0.0048%
      African/African American
      1 / 74,916
      0.0013%
      + 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      0.065% · 12 / 18,414
      0 hom · FAF 0.059%
      European (non-Finnish)
      12 / 11,736
      0.1%
      + 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      Error retrieving ClinVar entry.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.067. BayesDel score = -0.54419.
      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. CUX1, a transcription factor, is frequently altered in several cancers types by deletion, mutation or translocation.
      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 · 5 PMIDs not cited in assessment
      25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
      25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
      24121147 ↗ Appropriateness of newborn screening for α1-antitrypsin deficiency. CLINVAR
      23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
      24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR