Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
KMT2A
Final classification
Likely Benign
KMT2A c.7362T>C · p.Thr2454=
KMT2A

NM_005933.3:c.7362T>C is a synonymous variant (p.Thr2454=) in KMT2A. KMT2A loss-of-function variants cause Wiedemann-Steiner syndrome (autosomal dominant).

Gene
KMT2A
Transcript
NM_005933.3
HGVS · transcript:coding
NM_005933.3:c.7362T>C
Consequence
N/A
GRCh38
chr11:118503263 T>C
GRCh37
chr11:118373978 T>C
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, BP7 supporting; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
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, BP7 supporting; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP4BP7 Likely Benign
KMT2A c.7362T>C

NM_005933.3:c.7362T>C is a synonymous variant (p.Thr2454=) in KMT2A. KMT2A loss-of-function variants cause Wiedemann-Steiner syndrome (autosomal dominant).1 This variant is present at extremely low frequency in population databases (gnomAD v2.1: 2/282,756 alleles, AF=7.07e-06; gnomAD v4.1: 2/1,613,960 alleles, AF=1.24e-06), meeting PM2 at supporting level.2 SpliceAI predicts no splice impact (max delta=0.0; all four delta scores at 0.0), supporting a benign interpretation under BP4 and BP7.3 No pathogenic in silico predictions are available; REVEL and BayesDel scores were not found for this variant. No computational evidence supports a deleterious effect (PP3 not met).4 The variant is absent from ClinVar and no literature reports this specific variant. OncoKB lists classification as 'Unknown Oncogenic Effect' with no supporting evidence.5 Applying generic ACMG/AMP 2015 combination rules: PM2 (supporting pathogenic) is outweighed by BP4 (supporting benign) and BP7 (supporting benign), yielding a classification of Likely Benign (2 supporting benign criteria).6

PM2 + BP4 + BP7 Likely Benign
1 pvs1_gene_context
6 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 · 3 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 · supports benign
      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= 1.23919e-06; MAF= 0.00012%, 2/1613960 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.69488e-06; MAF= 0.00017%, 2/1180022 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.07324e-06; MAF= 0.00071%, 2/282756 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.54909e-05; MAF= 0.00155%, 2/129108 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00012% · 2 / 1,613,960
      0 hom · FAF 2.8e-05%
      European (non-Finnish)
      2 / 1,180,022
      0.00017%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.00071% · 2 / 282,756
      0 hom
      European (non-Finnish)
      2 / 129,108
      0.0015%
      + 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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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