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CDK12
Final classification
VUS
CDK12 c.2351G>A · p.Arg784Gln
CDK12

NM_016507.4:c.2351G>A (p.Arg784Gln) in CDK12 is a missense variant absent from ClinVar and present at extremely low frequency in population databases (gnomAD v2.1: 3/275,404 alleles, AF 0.00109%; gnomAD v4.1: 18/1,609,482 alleles, AF 0.00112%), meeting PM2 at supporting strength.

Gene
CDK12
Transcript
NM_016507.4
HGVS · transcript:coding
NM_016507.4:c.2351G>A
Consequence
N/A
GRCh38
chr17:39494626 G>A
GRCh37
chr17:37650879 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, BP4 supporting benign; 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 benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CDK12 c.2351G>A

NM_016507.4:c.2351G>A (p.Arg784Gln) in CDK12 is a missense variant absent from ClinVar and present at extremely low frequency in population databases (gnomAD v2.1: 3/275,404 alleles, AF 0.00109%; gnomAD v4.1: 18/1,609,482 alleles, AF 0.00112%), meeting PM2 at supporting strength.1 Multiple computational predictors support a benign effect: REVEL score 0.075 (strongly benign), BayesDel score −0.516897 (benign), and SpliceAI max delta 0.01 (no predicted splicing impact), meeting BP4 at supporting benign strength.2 No functional studies, de novo observations, segregation data, case-control data, or ClinVar classifications were available to support additional pathogenic or benign criteria.3 The variant is observed once somatically in COSMIC (COSV104713462) but this does not contribute to germline ACMG/AMP classification. The supporting pathogenic evidence (PM2) is balanced by supporting benign evidence (BP4). No other criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
3 oncokb ↗pvs1_variant_assessment
4 generic_acmg_combination_rules
Gene diagram · NM_016507.4 · variants mapped to exon structure
CDK12 NM_016507.4
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= 1.11837e-05; MAF= 0.00112%, 18/1609482 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 0.000156607; MAF= 0.01566%, 10/63854 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.08931e-05; MAF= 0.00109%, 3/275404 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000281452; MAF= 0.02815%, 2/7106 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0011% · 18 / 1,609,482
      0 hom · FAF 0.00025%
      European (Finnish)
      10 / 63,854
      0.016%
      Remaining individuals
      1 / 62,320
      0.0016%
      European (non-Finnish)
      7 / 1,177,366
      0.00059%
      + 7 not observed (Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0011% · 3 / 275,404
      0 hom
      Remaining individuals
      2 / 7,106
      0.028%
      European (non-Finnish)
      1 / 124,794
      0.0008%
      + 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      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 = 0.01). REVEL score = 0.075. BayesDel score = -0.516897.
      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. CDK12, a cyclin dependent kinase, is recurrently mutated in metastatic prostate and serous ovarian cancers.
      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 previously been reported in somatic cancers (COSMIC; COSV104713462, n = 1 times).
      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