Starting
Initialising…
0%
FH
Final classification
VUS
FH c.6C>T · p.Tyr2=
FH

NM_000143.4:c.6C>T is a synonymous variant (p.Tyr2=) in exon 1 of FH, which encodes fumarate hydratase. This variant is present in gnomAD at low overall frequency: 0.025% in v2.1 (45/178,374 alleles) and 0.013% in v4.1 (199/1,544,456 alleles), with grpmax filtering allele fractions of 0.018% and 0.029% respectively, meeting PM2 at supporting strength.

Gene
FH
Transcript
NM_000143.4
HGVS · transcript:coding
NM_000143.4:c.6C>T
Consequence
N/A
GRCh38
chr1:241519717 G>A
GRCh37
chr1:241683017 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, BP6 supporting; 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, BP6 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP6 VUS
FH c.6C>T

NM_000143.4:c.6C>T is a synonymous variant (p.Tyr2=) in exon 1 of FH, which encodes fumarate hydratase. This variant is present in gnomAD at low overall frequency: 0.025% in v2.1 (45/178,374 alleles) and 0.013% in v4.1 (199/1,544,456 alleles), with grpmax filtering allele fractions of 0.018% and 0.029% respectively, meeting PM2 at supporting strength.1 The variant has been classified as Benign or Likely benign by multiple reputable clinical laboratories in ClinVar (Variation ID 184570): 4 laboratories classify as Benign and 6 as Likely benign, with criteria provided. The consensus among established clinical testing laboratories meets BP6 at supporting benign strength.2 SpliceAI predicts no splicing impact (max delta score 0.00), and the variant does not lie within a known mutational hotspot or the fumarate lyase domain. No functional studies, cosegregation data, de novo reports, or case-control analyses are available for this variant.3 PVS1, PS1, PS5, PM5, PP2, BP1, BP3, PM3, and PM4 are not applicable to this synonymous variant. The remaining pathogenic criteria (PS2, PS3, PS4, PM1, PM6, PP1, PP3, PP4, PP5) are not met. All benign criteria except BP6 are not met or not assessed. BA1 and BS1 are not met as the overall allele frequency is below respective thresholds. The net evidence tally consists of one supporting pathogenic criterion (PM2_supporting) and one supporting benign criterion (BP6_supporting). Under ACMG/AMP 2015 combination rules (PMID:25741868), when benign and pathogenic criteria cancel at the supporting level, the variant defaults to Variant of Uncertain Significance (VUS).4

PM2 + BP6 VUS
4 generic_acmg_combination_rules
Gene diagram · NM_000143.4 · variants mapped to exon structure
FH NM_000143.4
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= 0.000128848; MAF= 0.01288%, 199/1544456 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00298204; MAF= 0.29820%, 85/28504 alleles, homozygotes = 0); grpmax FAF= 0.00028848.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000252279; MAF= 0.02523%, 45/178374 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00329334; MAF= 0.32933%, 28/8502 alleles, homozygotes = 0); grpmax FAF= 0.00017843.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.013% · 199 / 1,544,456
      0 hom · FAF 0.029%
      Ashkenazi Jewish
      85 / 28,504
      0.3%
      Middle Eastern
      2 / 4,578
      0.044%
      South Asian
      33 / 83,580
      0.039%
      Remaining individuals
      19 / 59,670
      0.032%
      East Asian
      6 / 40,706
      0.015%
      European (Finnish)
      7 / 59,102
      0.012%
      European (non-Finnish)
      46 / 1,143,940
      0.004%
      Admixed American
      1 / 50,768
      0.002%
      + 2 not observed (Amish, African/African American)
      gnomAD v2.1
      0.025% · 45 / 178,374
      0 hom · FAF 0.018%
      Ashkenazi Jewish
      28 / 8,502
      0.33%
      Remaining individuals
      2 / 5,282
      0.038%
      South Asian
      8 / 22,282
      0.036%
      East Asian
      3 / 12,262
      0.024%
      European (Finnish)
      1 / 18,642
      0.0054%
      European (non-Finnish)
      3 / 70,378
      0.0043%
      + 2 not observed (African/African American, Admixed American)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (6 clinical laboratories) and as Benign (4 clinical laboratories). (ClinVarID = 184570)
      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
      Triaged references · 9 PMIDs not cited in assessment
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      20301430 ↗ FH Tumor Predisposition Syndrome. CLINVAR
      24319509 ↗ Canadian guideline on genetic screening for hereditary renal cell cancers. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR
      26389510 ↗ Genetics of Renal Cell Carcinoma (PDQ®): Health Professional Version. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR