Starting
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KMT2A
Final classification
VUS
KMT2A c.2684A>G · p.Lys895Arg
KMT2A

NM_005933.3:c.2684A>G (p.Lys895Arg) is a missense variant in exon 3 of KMT2A, a gene associated with autosomal dominant Wiedemann-Steiner syndrome.

Gene
KMT2A
Transcript
NM_005933.3
HGVS · transcript:coding
NM_005933.3:c.2684A>G
Consequence
N/A
GRCh38
chr11:118473843 A>G
GRCh37
chr11:118344558 A>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, 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
KMT2A c.2684A>G

NM_005933.3:c.2684A>G (p.Lys895Arg) is a missense variant in exon 3 of KMT2A, a gene associated with autosomal dominant Wiedemann-Steiner syndrome. This variant is extremely rare in large population databases, with an allele frequency of 0.00283% in gnomAD v2.1 (8/282,230 alleles) and 0.00415% in gnomAD v4.1 (67/1,614,060 alleles), with no homozygotes observed. It is absent from gnomAD-Canada (PM2_Supporting).1 Multiple lines of computational evidence predict a benign effect: REVEL score 0.224 (benign range), BayesDel score -0.154507 (benign), and SpliceAI predicts no splicing impact with a maximum delta score of 0.02 (BP4_Supporting).2 This variant has been reported in ClinVar (Variation ID 1335086) with conflicting classifications: Uncertain significance by Invitae and Likely benign by CeGaT Center for Human Genetics Tuebingen. Neither submission reaches a definitive pathogenic or benign classification.3 The only publication associated with ClinVar submissions (PMID 28492532, Sherloc classification framework) does not mention this specific variant; it was reviewed in full text and confirmed to be a methodology reference only.4 This variant has been reported in COSMIC (COSV63290798) in 4 somatic cancer samples, but this does not constitute germline disease evidence. Several potentially relevant publications were identified by exploratory literature search (de novo report, functional studies, cosegregation data, domain hotspot analysis) but none of the associated PMIDs are present in the case directory for verification; these criteria (PS2, PS3, PS4, PM1, PM6, PP1, BS3) remain not assessed pending full-text retrieval and verification. Applying the generic ACMG/AMP 2015 combination rules (PMID 25741868): the criteria met are PM2_Supporting (pathogenic) and BP4_Supporting (benign). These are conflicting at the supporting level and are insufficient to reach a likely pathogenic or likely benign classification. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_005933.3 · variants mapped to exon structure
KMT2A NM_005933.3
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= 4.15102e-05; MAF= 0.00415%, 67/1614060 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000164366; MAF= 0.01644%, 1/6084 alleles, homozygotes = 0); grpmax FAF= 4.264e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 2.83457e-05; MAF= 0.00283%, 8/282230 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.22248e-05; MAF= 0.00622%, 8/128566 alleles, homozygotes = 0); grpmax FAF= 2.867e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0042% · 67 / 1,614,060
      0 hom · FAF 0.0043%
      Middle Eastern
      1 / 6,084
      0.016%
      European (non-Finnish)
      63 / 1,180,034
      0.0053%
      Remaining individuals
      3 / 62,490
      0.0048%
      + 7 not observed (Admixed American, European (Finnish), Amish, East Asian, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0028% · 8 / 282,230
      0 hom · FAF 0.0029%
      European (non-Finnish)
      8 / 128,566
      0.0062%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (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 Uncertain significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 1335086)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.224. BayesDel score = -0.154507.
      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. KMT2A, a histone methyltransferase, is altered by mutation or deletion in various solid tumors, and by chromosomal rearrangement in various hematologi
      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; COSV63290798, n = 4 times).
      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 · 1 PMID not cited in assessment
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR