Starting
Initialising…
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HOXB13
Final classification
VUS
HOXB13 c.567C>T · p.Asn189=
HOXB13

NM_006361.6:c.567C>T is a synonymous variant in HOXB13 (p.Asn189=) that does not alter the amino acid sequence.

Gene
HOXB13
Transcript
NM_006361.6
HGVS · transcript:coding
NM_006361.6:c.567C>T
Consequence
N/A
GRCh38
chr17:48728027 G>A
GRCh37
chr17:46805389 G>A
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, BP6 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
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, BP6 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
Classification rationale
PM2 BP6 VUS
HOXB13 c.567C>T

NM_006361.6:c.567C>T is a synonymous variant in HOXB13 (p.Asn189=) that does not alter the amino acid sequence. This variant is extremely rare in population databases, present at an allele frequency of 0.00991% in gnomAD v2.1 (28/282,626 alleles) and 0.00452% in gnomAD v4.1 (73/1,614,196 alleles), with no homozygotes observed, satisfying PM2 at supporting level.1 Multiple reputable clinical diagnostic laboratories (8 independent submissions) have classified this variant as Benign or Likely benign in ClinVar (VariationID 483492), with the underlying variant-specific evidence not publicly available for independent evaluation, satisfying BP6 at supporting level.2 SpliceAI predicts no splicing impact (max delta score = 0.00), consistent with the synonymous nature of this variant.3 No functional studies, cosegregation data, de novo observations, case-control studies, or computational evidence supporting pathogenicity have been identified for this variant. The variant lies at codon 189, outside the HOXB13 homeodomain (aa 195-254), and does not fall within a known mutational hotspot or functionally critical domain. Bulk evidence is sparse: one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP6) are met, yielding a net indeterminate ACMG/AMP classification by strict criteria counting. However, the unanimous benign/likely benign consensus from 8 independent clinical laboratories strongly supports a benign interpretation.4

PM2 + BP6 VUS
Gene diagram · NM_006361.6 · variants mapped to exon structure
HOXB13 NM_006361.6
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
      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= 4.52238e-05; MAF= 0.00452%, 73/1614196 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.00074611; MAF= 0.07461%, 56/75056 alleles, homozygotes = 0); grpmax FAF= 0.00058932.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 9.90709e-05; MAF= 0.00991%, 28/282626 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.00100152; MAF= 0.10015%, 25/24962 alleles, homozygotes = 0); grpmax FAF= 0.00071547.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0045% · 73 / 1,614,196
      0 hom · FAF 0.059%
      African/African American
      56 / 75,056
      0.075%
      Middle Eastern
      1 / 6,062
      0.016%
      Admixed American
      8 / 60,030
      0.013%
      Remaining individuals
      7 / 62,510
      0.011%
      European (Finnish)
      1 / 64,028
      0.0016%
      + 5 not observed (Amish, East Asian, South Asian, Ashkenazi Jewish, European (non-Finnish))
      gnomAD v2.1
      0.0099% · 28 / 282,626
      0 hom · FAF 0.072%
      African/African American
      25 / 24,962
      0.1%
      Admixed American
      3 / 35,432
      0.0085%
      + 6 not observed (Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Benign (3 clinical laboratories) and as benign (1 clinical laboratory). (ClinVarID = 483492)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 PMIDs not cited in assessment
      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
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR