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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 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present at extremely low frequency in population databases. In gnomAD v2.1, the allele frequency is 0.00991% (28/282,626 alleles, 0 homozygotes; grpmax FAF=0.0715%). In gnomAD v4.1, the allele frequency is 0.00452% (73/1,614,196 alleles, 0 homozygotes; grpmax FAF=0.0589%). Both global AF and grpmax FAF are well below the 0.1% threshold for PM2. It is absent from gnomAD-Canada v1.0. The highest sub-population frequency is in the African/African American population (v2.1: 0.10%, v4.1: 0.075%).
gnomAD v2.1: AF=0.00991% (28/2826260 hom)
BP6 supporting Benign
Multiple reputable clinical diagnostic laboratories have independently classified NM_006361.6:c.567C>T as Benign or Likely benign in ClinVar (VariationID 483492). Specifically: 4 clinical laboratories classify as Likely benign (GeneDx, Ambry Genetics, KCCC/NGS Laboratory, Sinai Health System), 3 as Benign (Labcorp/Women's Health and Genetics, Myriad Genetics), and 1 as benign (Quest Diagnostics). These are established clinical testing laboratories with criteria-provided classifications. The underlying variant-specific evidence used by these laboratories is not publicly available for independent evaluation, satisfying the BP6 requirement.
ClinVar VariationID 483492: Likely benign by 4 clinical labs (GeneDxAmbry GeneticsKCCC
Assessed · not applied
Pathogenic
PS2 No de novo occurrences of NM_006361.6:c.567C>T have been reported in ClinVar, the published literature, or public databases.
PS3 No well-established in vitro or in vivo functional studies have been published demonstrating a damaging effect of c.567C>T on HOXB13 protein function or splicing.
PS4 No case-control studies have been identified comparing the prevalence of c.567C>T in affected individuals versus controls for any HOXB13-associated phenotype (e.g., prostate cancer).
PM1 The variant is located at codon 189 (Asn189), which lies outside the HOXB13 homeodomain (amino acids 195-254).
PM6 No reported instances of de novo occurrence of c.567C>T (without confirmation of paternity and maternity) have been identified in ClinVar, the published literature, or public databases.
PP1 No published cosegregation data have been identified for c.567C>T with any HOXB13-associated disease phenotype.
PP3 Multiple lines of in silico evidence do not support a deleterious effect.
PP4 No patient-specific phenotype or family history data are available to evaluate whether the clinical presentation is highly specific for a disease with a single genetic etiology.
PP5 PP5 requires a reputable source to have recently reported the variant as pathogenic with evidence not available for independent evaluation.
Benign
BA1 The maximum allele frequency observed in any population is 0.10% (African/African American, gnomAD v2.1), which is well below the 1% threshold for BA1.
BS1 The maximum allele frequency observed is 0.10% (African/African American, gnomAD v2.1), which is below the 0.3% threshold for BS1 under non-VCEP generic ACMG rules.
BS2 No specific observations of this variant in healthy adult individuals for a disorder with full penetrance expected at an early age have been identified.
BS3 No well-established in vitro or in vivo functional studies have been published demonstrating that c.567C>T has no damaging effect on HOXB13 protein function or mRNA splicing.
BS4 No published family segregation analyses demonstrating lack of segregation of c.567C>T with an HOXB13-associated phenotype have been identified.
BP2 No reported observations of c.567C>T in trans with a known pathogenic HOXB13 variant (for a dominant disorder) or in cis with a pathogenic variant in any inheritance pattern.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
BP7 BP7 requires both (1) splicing prediction algorithms predict no impact to the splice consensus sequence nor creation of a new splice site, AND (2) the nucleotide is not highly conserved.
N/A · 5 PVS1 · PS1 · PM5 · PP2 · BP1
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