Analysis in progress
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This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
AR
Final classification
VUS
AR c.455C>T · p.Pro152Leu
AR

NM_000044.4:c.455C>T (p.Pro152Leu) in AR is a missense variant in the N-terminal transactivation domain.

Gene
AR
Transcript
NM_000044.4
HGVS · transcript:coding
NM_000044.4:c.455C>T
Consequence
N/A
GRCh38
chrX:67545601 C>T
GRCh37
chrX:66765443 C>T
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; combination = 1 supporting + 1 supporting benign, which maps to VUS.
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; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
AR c.455C>T

NM_000044.4:c.455C>T (p.Pro152Leu) in AR is a missense variant in the N-terminal transactivation domain. This variant is extremely rare in population databases: absent from gnomAD v2.1 and gnomAD-Canada, and present in gnomAD v4.1 at an allele frequency of 8.42 × 10⁻⁷ (1/1,187,892 alleles), fulfilling PM2 at supporting strength.1 In silico predictions are concordantly benign: BayesDel scores -0.012 (benign range) and SpliceAI predicts no splicing alteration (max delta = 0.00), supporting BP4 at supporting level.2 One supporting pathogenic criterion (PM2_supporting) and one supporting benign criterion (BP4_supporting) offset each other. The variant is absent from ClinVar, has no functional data, and no literature reports.3 Insufficient evidence to classify as pathogenic or benign. Overall classification: Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 framework.4

PM2 + BP4 VUS
2 bayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_000044.4 · variants mapped to exon structure
AR NM_000044.4
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
      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= 8.41827e-07; MAF= 0.00008%, 1/1187892 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.13202e-06; MAF= 0.00011%, 1/883379 alleles, homozygotes = 0).
      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
      8.4e-05% · 1 / 1,187,892
      0 hom
      European (non-Finnish)
      1 / 883,379
      0.00011%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = -0.0120934.
      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. AR (androgen receptor), a transcription factor, is most frequently altered in advanced or castration-resistant prostate cancer.
      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