Starting
Initialising…
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MEN1
Final classification
Benign
MEN1 c.435C>T · p.Ser145=
MEN1

NM_000244.3:c.435C>T is a synonymous variant (p.Ser145=) in exon 2 of the MEN1 gene.

Gene
MEN1
Transcript
NM_000244.3
HGVS · transcript:coding
NM_000244.3:c.435C>T
Consequence
N/A
GRCh38
chr11:64809675 G>A
GRCh37
chr11:64577147 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: BA1 stand-alone benign, BS1 strong benign, BS2 supporting benign, BP2 supporting benign, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 1 stand-alone benign + 1 strong benign + 5 supporting benign, which maps to 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: BA1 stand-alone benign, BS1 strong benign, BS2 supporting benign, BP2 supporting benign, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 1 stand-alone benign + 1 strong benign + 5 supporting benign, which maps to Benign.
Classification rationale
BA1BS1BS2BP2BP4BP6BP7 Benign
MEN1 c.435C>T

NM_000244.3:c.435C>T is a synonymous variant (p.Ser145=) in exon 2 of the MEN1 gene. This variant is present at a high allele frequency in population databases: 2.84% overall in gnomAD v2.1 (8021/282758 alleles, 189 homozygotes) and 3.54% in gnomAD v4.1 (57090/1614046 alleles, 1240 homozygotes), with a maximum subpopulation frequency of 6.39% in the European (Finnish) population. This far exceeds the BA1 threshold of >1%, satisfying stand-alone benign evidence.1 The variant has been observed in a homozygous state in 189 individuals in gnomAD v2.1 and 1240 individuals in gnomAD v4.1. For a highly penetrant autosomal dominant disorder such as MEN1, the observation of multiple healthy adult homozygotes is incompatible with pathogenicity.2 SpliceAI predicts no splice impact (max delta score = 0.00), consistent with a silent synonymous change that does not alter normal splicing.3 ClinVar classifies this variant as Benign, with consensus across 18 clinical laboratories (ClinVar ID 96252).4 No pathogenic evidence was identified: no de novo occurrences, no functional studies demonstrating damage, no case-control enrichment, no cosegregation data, and no in silico predictions of pathogenicity. Under generic ACMG/AMP 2015 rules, BA1 (stand-alone benign) alone is sufficient for a Benign classification. The additional supporting benign criteria (BS2, BP2, BP4, BP6, BP7) further reinforce the benign interpretation.5

BA1 + BS1 + BS2 + BP2 + BP4 + BP6 + BP7 Benign
Gene diagram · NM_000244.3 · variants mapped to exon structure
MEN1 NM_000244.3
Fetching transcript structure from UCSC…
Applied criteria · 7 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= 0.0353707; MAF= 3.53707%, 57090/1614046 alleles, homozygotes = 1240) and has highest observed frequency in the European (Finnish) population (AF= 0.0637514; MAF= 6.37514%, 4082/64030 alleles, homozygotes = 142); grpmax FAF= 0.0413118.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.028367; MAF= 2.83670%, 8021/282758 alleles, homozygotes = 189) and has highest observed frequency in the European (Finnish) population (AF= 0.0639331; MAF= 6.39331%, 1606/25120 alleles, homozygotes = 63); grpmax FAF= 0.0423484.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      3.5% · 57090 / 1,614,046
      1240 hom · FAF 4.1%
      European (Finnish)
      4082 / 64,030
      6.4%
      142 hom
      European (non-Finnish)
      49109 / 1,179,924
      4.2%
      1049 hom
      Amish
      37 / 912
      4.1%
      1 hom
      Remaining individuals
      1751 / 62,498
      2.8%
      36 hom
      Middle Eastern
      75 / 6,062
      1.2%
      3 hom
      Admixed American
      614 / 60,020
      1%
      5 hom
      South Asian
      694 / 91,084
      0.76%
      2 hom
      Ashkenazi Jewish
      207 / 29,604
      0.7%
      2 hom
      African/African American
      517 / 75,036
      0.69%
      East Asian
      4 / 44,876
      0.0089%
      gnomAD v2.1
      2.8% · 8021 / 282,758
      189 hom · FAF 4.2%
      European (Finnish)
      1606 / 25,120
      6.4%
      63 hom
      European (non-Finnish)
      5315 / 129,094
      4.1%
      110 hom
      Remaining individuals
      233 / 7,218
      3.2%
      7 hom
      Admixed American
      376 / 35,424
      1.1%
      6 hom
      Ashkenazi Jewish
      81 / 10,368
      0.78%
      2 hom
      South Asian
      234 / 30,614
      0.76%
      1 hom
      African/African American
      173 / 24,968
      0.69%
      East Asian
      3 / 19,952
      0.015%
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (18 clinical laboratories). (ClinVarID = 96252)
      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 previously been reported in somatic cancers (COSMIC; COSV56341605, n = 2 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 · 9 PMIDs not cited in assessment
      10090472 ↗ Germline mutations in the multiple endocrine neoplasia type 1 gene: evidence for frequent splicing defects. CLINVAR
      10634422 ↗ Complete sequencing and messenger ribonucleic acid expression analysis of the MEN I gene in adrenal cancer. CLINVAR
      10843194 ↗ Familial hypercalcemia and hypercalciuria caused by a novel mutation in the cytoplasmic tail of the calcium receptor. CLINVAR
      11807402 ↗ Familial isolated hyperparathyroidism: clinical and genetic characteristics of 36 kindreds. CLINVAR
      17623761 ↗ Clinical testing for mutations in the MEN1 gene in Sweden: a report on 200 unrelated cases. CLINVAR
      17953629 ↗ MEN1 gene mutations in Hungarian patients with multiple endocrine neoplasia type 1. CLINVAR
      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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR