Variant classification summary

NM_000143.4:c.6C>T

FH · NP_000134.2:p.(Tyr2=) · NM_000143.4

GRCh37: chr1:241683017 G>A · GRCh38: chr1:241519717 G>A

Gene: FH Transcript: NM_000143.4

Final call

VUS

PM2 supporting BP6 supporting

Variant details

Gene

FH

Transcript

NM_000143.4

Protein

NP_000134.2:p.(Tyr2=)

gnomAD AF

0.0001288479568210425 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

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.

5

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).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_000143.4:c.6C>T is a synonymous substitution encoding p.Tyr2= (no amino acid change) and does not fall into null-variant buckets (nonsense, frameshift, or canonical ±1,2 splice consensus) defined for PVS1 per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework pvs1_variant_assessment
PS1	N/A	PS1 applies when the same amino acid change has been previously established as pathogenic regardless of nucleotide change. NM_000143.4:c.6C>T is a synonymous variant (p.Tyr2=) with no amino acid change; therefore PS1 does not apply.
PS2	Not met	No de novo occurrence of NM_000143.4:c.6C>T has been reported in the literature or ClinVar submissions; exploratory literature search found no de novo reports.
PS3	Not met	No well-established in vitro or in vivo functional studies have been identified for NM_000143.4:c.6C>T. REVEL and BayesDel do not score synonymous variants. No published functional assays assessing splicing, enzyme activity, or protein expression for this variant.	clinvar
PS4	Not met	No published case-control studies compare the prevalence of NM_000143.4:c.6C>T in FH-related disease (HLRCC) patients versus controls. Population frequency in gnomAD alone does not satisfy PS4 without statistical enrichment analysis in affected individuals.	gnomad_v2 gnomad_v4
PS5	N/A	PS5 requires a novel missense change at an amino acid residue where a different missense change has been established as pathogenic. NM_000143.4:c.6C>T is a synonymous variant with no amino acid change, and no pathogenic missense variant has been established at codon 2 (Tyr2).
PM1	Not met	NM_000143.4:c.6C>T resides in exon 1 (residue Tyr2), outside the fumarate lyase domain (exons 5-7) that harbors established mutational hotspots for FH in HLRCC. No clustering of pathogenic variants at this residue has been reported.
PM2	Met	NM_000143.4:c.6C>T is present in gnomAD at very low overall allele frequency: 0.025% in v2.1 (45/178374 alleles, grpmax FAF 0.018%) and 0.013% in v4.1 (199/1544456 alleles, grpmax FAF 0.029%). Both overall AF and grpmax FAF are below the 0.1% threshold. No homozygotes observed. Not detected in gnomAD-Canada. Caveat: Ashkenazi Jewish subpopulation AF is 0.33% (v2.1) / 0.30% (v4.1), exceeding the 0.1% cutoff, but the controlling grpmax FAF remains below threshold.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 requires a different missense change at the same amino acid residue as an established pathogenic missense variant. NM_000143.4:c.6C>T is a synonymous variant (p.Tyr2=) with no amino acid change and no residue context suitable for classic PM5 semantics.	pm5_candidates
PM6	Not met	No de novo reports for NM_000143.4:c.6C>T; no maternity/paternity confirmation data available. Exploratory literature search found no de novo observations.
PP1	Not met	No cosegregation studies have been published for NM_000143.4:c.6C>T in affected families. Exploratory search found no segregation data.
PP2	N/A	PP2 is defined for missense variants in genes where missense variants are a common mechanism of disease and benign missense variation is rare. NM_000143.4:c.6C>T is a synonymous variant, not a missense variant; PP2 does not apply.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. REVEL and BayesDel do not score synonymous variants (both returned not found). SpliceAI predicts no splicing impact (max delta 0.00). No HCI prior score available for FH. No computational evidence supports pathogenicity.	spliceai
PP4	Not met	No detailed phenotypic data available for patients carrying NM_000143.4:c.6C>T. The variant's phenotype specificity or family history cannot be assessed from available sources.	clinvar
PP5	Not met	PP5 requires a reputable source to report the variant as pathogenic with evidence unavailable for independent evaluation. ClinVar reports NM_000143.4:c.6C>T as Likely benign (6 clinical laboratories) and Benign (4 clinical laboratories). No reputable source reports it as pathogenic.	clinvar
BA1	Not met	NM_000143.4:c.6C>T overall allele frequency in gnomAD is 0.025% (v2.1) and 0.013% (v4.1), both well below the 1% BA1 threshold. Not applicable as a stand-alone benign criterion.	gnomad_v2 gnomad_v4
BS1	Not met	NM_000143.4:c.6C>T overall allele frequency in gnomAD is 0.025% (v2.1, grpmax FAF 0.018%) and 0.013% (v4.1, grpmax FAF 0.029%), both below the 0.3% BS1 threshold. The Ashkenazi Jewish subpopulation AF is elevated at 0.33% (v2.1) / 0.30% (v4.1), but the controlling grpmax FAF remains below threshold for a dominant disorder.	gnomad_v2 gnomad_v4
BS2	Not met	The variant is observed in heterozygous state in gnomAD population databases (45-199 alleles). However, BS2 requires observation in a healthy adult individual for a disorder with complete penetrance expected at an early age. HLRCC has variable penetrance and later onset; gnomAD observation alone does not satisfy BS2. For the recessive FH deficiency context, no homozygotes are observed.	gnomad_v2 gnomad_v4
BS3	Not met	No well-characterized functional studies demonstrate a neutral effect for NM_000143.4:c.6C>T. No in vitro or in vivo assays assessing splicing, enzyme activity, or protein expression exist for this variant. The SpliceAI prediction (delta 0.00) is in silico only and does not constitute a functional study.	spliceai
BS4	Not met	No cosegregation data demonstrating non-segregation of NM_000143.4:c.6C>T with disease in affected families. Exploratory search found no relevant family studies.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants are known to cause disease. NM_000143.4:c.6C>T is a synonymous variant, not a missense variant; BP1 does not apply.
BP2	Not met	No published instance of a healthy individual carrying NM_000143.4:c.6C>T in trans with a known pathogenic FH variant. gnomAD shows no homozygotes, and no compound heterozygous reports exist for FH deficiency cases.	gnomad_v2 gnomad_v4
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without known function. Not applicable to a single-nucleotide synonymous substitution.
BP4	Not met	Multiple lines of computational evidence are insufficient to support no impact. REVEL and BayesDel are not designed for synonymous variants (both returned not found). SpliceAI predicts no splicing impact (delta 0.00), but this single line of in silico evidence does not meet the 'multiple lines' requirement for BP4.	spliceai
BP5	Not met	No cases have been reported where NM_000143.4:c.6C>T was found in a patient with an alternate molecular basis for disease. No such data available in ClinVar or published literature.
BP6	Met	Multiple reputable clinical laboratories have independently classified NM_000143.4:c.6C>T as benign or likely benign in ClinVar (4 labs Benign, 6 labs Likely benign; 9 usable submissions with criteria provided). While the specific evidence supporting their classifications is not publicly available for independent evaluation, the consensus among established clinical testing laboratories meets BP6 at supporting benign strength.	clinvar
BP7	Not assessed	BP7 requires both (a) splicing prediction algorithms predict no impact to splice consensus or creation of new splice site, AND (b) the nucleotide is not highly conserved. SpliceAI delta 0.00 satisfies condition (a), but nucleotide-level conservation data for position c.6 in FH exon 1 is not available. Cannot fully assess BP7 without conservation information.	spliceai
PM3	N/A	Skipped per user directive — trivially not applicable.
PM4	N/A	Skipped per user directive — trivially not applicable.

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