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KMT2B
Final classification
VUS
KMT2B c.5989C>G · p.Leu1997Val
KMT2B

NM_014727.2:c.5989C>G (p.Leu1997Val) in KMT2B is extremely rare in population databases, observed in only 1 of 1,613,902 alleles (AF=0.00006%) in gnomAD v4.1 and absent from gnomAD v2.1 and gnomAD-Canada, meeting PM2 at supporting strength.

Gene
KMT2B
Transcript
NM_014727.2
HGVS · transcript:coding
NM_014727.2:c.5989C>G
Consequence
N/A
GRCh38
chr19:35732538 C>G
GRCh37
chr19:36223439 C>G
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; combination = 1 supporting, 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
KMT2B c.5989C>G

NM_014727.2:c.5989C>G (p.Leu1997Val) in KMT2B is extremely rare in population databases, observed in only 1 of 1,613,902 alleles (AF=0.00006%) in gnomAD v4.1 and absent from gnomAD v2.1 and gnomAD-Canada, meeting PM2 at supporting strength.1 This variant is a missense substitution and does not qualify for PVS1; no pathogenic variants have been reported at the same residue (PS1 not met); no functional studies exist (PS3 not assessed); and no de novo or segregation data are available. Multiple in silico prediction tools do not support a deleterious effect: REVEL score is 0.37 (intermediate), BayesDel score is -0.166 (benign range), and SpliceAI predicts no splicing impact (max delta=0.00). However, this evidence is mixed and does not confidently meet PP3 or BP4.2 The only criterion met is PM2 (supporting). Per ACMG/AMP 2015 classification rules (PMID:25741868), a single supporting pathogenic criterion without any benign criteria is insufficient for a likely pathogenic or benign classification.3 Overall classification: Variant of Uncertain Significance (VUS). Additional evidence including functional studies, segregation analysis, case-control data, or clinical correlation is required to resolve the significance of this variant.

PM2 VUS
2 revelbayesdelspliceai ↗
3 generic_acmg_combination_rules
Gene diagram · NM_014727.2 · variants mapped to exon structure
KMT2B NM_014727.2
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 6.19616e-07; MAF= 0.00006%, 1/1613902 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47544e-07; MAF= 0.00008%, 1/1179880 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
      6.2e-05% · 1 / 1,613,902
      0 hom
      European (non-Finnish)
      1 / 1,179,880
      8.5e-05%
      + 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). REVEL score = 0.37. BayesDel score = -0.166046.
      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. KMT2B, a histone methyltransferase, is mutated at low frequencies in various cancer types.
      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