Starting
Initialising…
0%
POLE
Final classification
VUS
POLE c.1687-18G>A · p.?
POLE

NM_006231.4:c.1687-18G>A is a noncanonical intronic POLE variant observed in gnomAD v4.1 at 8/1447042 alleles (AF 5.52852e-06; 0.00055%), with the highest frequency in South Asians at 4/85948 alleles (AF 4.65398e-05; 0.00465%), which is below the non-VCEP PM2 threshold of 0.1%.

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.1687-18G>A
Consequence
N/A
GRCh38
chr12:132672340 C>T
GRCh37
chr12:133248926 C>T
Basis generic_acmg_2015_with_non_vcep_frequency_thresholds
generic_acmg_2015_with_non_vcep_frequency_thresholds
Classification rationale
PM2 BP4 VUS
POLE c.1687-18G>A

NM_006231.4:c.1687-18G>A is a noncanonical intronic POLE variant observed in gnomAD v4.1 at 8/1447042 alleles (AF 5.52852e-06; 0.00055%), with the highest frequency in South Asians at 4/85948 alleles (AF 4.65398e-05; 0.00465%), which is below the non-VCEP PM2 threshold of 0.1%.1 Population data are similarly rare in gnomAD v2.1 at 3/251248 alleles (AF 1.19404e-05; 0.00119%), with the highest South Asian frequency at 1/30616 alleles (AF 3.26627e-05; 0.00327%), and these values also remain below the BS1 threshold of 0.3% and BA1 threshold of 1%.2 SpliceAI predicts a maximum delta score of 0.01, which is below the 0.2 threshold commonly used to indicate splice-impact concern and supports a benign computational assessment under BP4 rather than pathogenic computational evidence.3 ClinVar contains a single submitter classification of Likely benign, which is directionally consistent with the splice prediction but is not used here as a standalone ACMG criterion.4 With conflicting supporting evidence from rarity and benign computational data, and without stronger pathogenic or benign evidence, NM_006231.4:c.1687-18G>A is classified as a Variant of Uncertain Significance.

PM2 + BP4 VUS
Gene diagram · NM_006231.4 · variants mapped to exon structure
POLE NM_006231.4
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= 5.52852e-06; MAF= 0.00055%, 8/1447042 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 4.65398e-05; MAF= 0.00465%, 4/85948 alleles, homozygotes = 0); grpmax FAF= 1.586e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.19404e-05; MAF= 0.00119%, 3/251248 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26627e-05; MAF= 0.00327%, 1/30616 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00055% · 8 / 1,447,042
      0 hom · FAF 0.0016%
      South Asian
      4 / 85,948
      0.0047%
      East Asian
      1 / 39,638
      0.0025%
      Admixed American
      1 / 44,706
      0.0022%
      European (non-Finnish)
      2 / 1,098,652
      0.00018%
      + 5 not observed (Remaining individuals, European (Finnish), Middle Eastern, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0012% · 3 / 251,248
      0 hom
      South Asian
      1 / 30,616
      0.0033%
      Admixed American
      1 / 34,580
      0.0029%
      European (non-Finnish)
      1 / 113,702
      0.00088%
      + 5 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      Sources & reference links
      5Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB