Starting
Initialising…
0%
SLC2A2
Final classification
VUS
SLC2A2 c.1094G>A · p.Arg365Gln
SLC2A2

PVS1 is not applicable. NM_000340.2:c.1094G>A is a missense variant (p.Arg365Gln), not a null variant meeting ClinGen SVI PVS1 criteria.

Gene
SLC2A2
Transcript
NM_000340.2
HGVS · transcript:coding
NM_000340.2:c.1094G>A
Consequence
N/A
GRCh38
chr3:170999141 C>T
GRCh37
chr3:170716930 C>T
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, PP3 supporting; combination = 2 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, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
SLC2A2 c.1094G>A

PVS1 is not applicable. NM_000340.2:c.1094G>A is a missense variant (p.Arg365Gln), not a null variant meeting ClinGen SVI PVS1 criteria.1 PM2 (Supporting) is met. The variant is present in gnomAD at extremely low frequency — v2.1 AF 2.13e-05 (6/282,168 alleles), v4.1 AF 1.99e-05 (32/1,611,868 alleles), grpmax FAF 1.13e-05 to 8.17e-05 — well below the 0.1% threshold. Absent from gnomAD-Canada. Zero homozygotes observed.2 PP3 (Supporting) is met. Multiple computational predictors support a deleterious effect: REVEL score 0.84 (strongly pathogenic range, >0.5), BayesDel no-AF score 0.352 (above deleterious threshold >0.27). SpliceAI predicts no splicing impact (delta 0.0), consistent with a coding missense variant.3 No pathogenic criteria beyond PM2 and PP3 (both supporting) are met. No benign criteria are met. All moderate, strong, and very strong criteria are either not applicable, not assessed, or not met. Per ACMG/AMP 2015 combination rules (PMID:25741868), two supporting pathogenic criteria (PM2_Supporting + PP3_Supporting) are insufficient to reach Likely Pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + PP3 VUS
3 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_000340.2 · variants mapped to exon structure
SLC2A2 NM_000340.2
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= 1.98527e-05; MAF= 0.00199%, 32/1611868 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000147043; MAF= 0.01470%, 11/74808 alleles, homozygotes = 0); grpmax FAF= 8.165e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 2.12639e-05; MAF= 0.00213%, 6/282168 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 4.00609e-05; MAF= 0.00401%, 1/24962 alleles, homozygotes = 0); grpmax FAF= 1.125e-05.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.002% · 32 / 1,611,868
      0 hom · FAF 0.0082%
      African/African American
      11 / 74,808
      0.015%
      Admixed American
      3 / 59,886
      0.005%
      European (non-Finnish)
      18 / 1,178,350
      0.0015%
      + 7 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0021% · 6 / 282,168
      0 hom · FAF 0.0011%
      African/African American
      1 / 24,962
      0.004%
      European (non-Finnish)
      5 / 128,674
      0.0039%
      + 6 not observed (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). REVEL score = 0.84. BayesDel score = 0.351945.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      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; COSV100049434, 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