Starting
Initialising…
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PMS2
Final classification
Uncertain Significance - Conflicting Evidence
PMS2 c.14A>T · p.Glu5Val
PMS2

NM_000535.7:c.14A>T (p.Glu5Val) is a missense variant in exon 1 of PMS2. It is extremely rare in population databases (gnomAD v4.1: 8/1,612,464 alleles, AF=4.96e-06), meeting PM2_Supporting per InSiGHT/ClinGen PMS2 VCEP v2.0.0.

Gene
PMS2
Transcript
NM_000535.7
HGVS · transcript:coding
NM_000535.7:c.14A>T
Consequence
N/A
GRCh38
chr7:6009006 T>A
GRCh37
chr7:6048637 T>A
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 Uncertain Significance - Conflicting Evidence
PMS2 c.14A>T

NM_000535.7:c.14A>T (p.Glu5Val) is a missense variant in exon 1 of PMS2. It is extremely rare in population databases (gnomAD v4.1: 8/1,612,464 alleles, AF=4.96e-06), meeting PM2_Supporting per InSiGHT/ClinGen PMS2 VCEP v2.0.0.1 Multiple in silico predictors support a benign effect: the HCI prior probability for pathogenicity is 0.004 (meeting BP4_Supporting), REVEL score is 0.498, BayesDel score is 0.008, and SpliceAI predicts no splicing impact (max delta = 0.00).2 No functional data, segregation data, de novo observations, or tumor phenotype data (MSI/IHC) are available for this variant. ClinVar reports this variant as Uncertain Significance (VCV231310, 7 submitters, criteria provided single submitter).3 The variant does not meet criteria for PVS1 (missense, not a null variant), PS1 (no same-amino-acid pathogenic comparator), PS3 (no functional data), PM5 (no same-residue pathogenic comparator), or any other pathogenic criterion. The only criteria met are PM2_Supporting (extremely rare in gnomAD) and BP4_Supporting (benign in silico predictions including HCI prior <0.11). With one pathogenic supporting and one benign supporting criterion, the evidence is insufficient to reach a Likely Pathogenic or Likely Benign classification under the VCEP combining rules. The variant remains a Variant of Uncertain Significance.4

PM2 + BP4 Uncertain Significance - Conflicting Evidence
2 hci_priorrevelbayesdelspliceai ↗
Gene diagram · NM_000535.7 · variants mapped to exon structure
PMS2 NM_000535.7
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
      Population frequency
      Overall AF
      8 / 1,612,464
      0.0005%
      Highest · European (non-Finnish)
      0.00068%
      Homozygotes
      0
      grpmax FAF
      0.00029%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 8 / 1,179,840 0.00068% 0
      Admixed American 0 / 60,008
      European (Finnish) 0 / 63,770
      Amish 0 / 912
      East Asian 0 / 44,890
      Middle Eastern 0 / 5,166
      South Asian 0 / 91,022
      Ashkenazi Jewish 0 / 29,604
      African/African American 0 / 74,896
      This variant is present in gnomAD v4.1 (AF= 4.96135e-06; MAF= 0.00050%, 8/1612464 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.78058e-06; MAF= 0.00068%, 8/1179840 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (6 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 231310)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.498. BayesDel score = 0.00801122. HCI prior probability for pathogenicity = 0.004. Custom PP2 score = 0.062.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PMS2, an endonuclease involved in DNA repair, is altered in various cancers.
      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.
      Literature · 22 PMIDs triaged · 8 high-priority
      22papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      24362816 ↗ functional
      Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.
      The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated g
      BS3PM1PS3
      25070057 ↗ segregation
      Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer.
      The Multi-Society Task Force, in collaboration with invited experts, developed guidelines to assist health care providers with the appropriate provision of genetic testing and management of patients at risk for and affected with Lynch syndrome as follows: Figure 1 provides a colorectal cancer risk assessment tool to screen individuals in the office or endoscopy setting; Figure 2 illustrates a stra
      BS4PP1PP5PS4
      25645574 ↗ splicing rna
      ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes.
      This guideline presents recommendations for the management of patients with hereditary gastrointestinal cancer syndromes. The initial assessment is the collection of a family history of cancers and premalignant gastrointestinal conditions and should provide enough information to develop a preliminary determination of the risk of a familial predisposition to cancer. Age at diagnosis and lineage (ma
      BP7PP3PP5PS4PVS1
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      31672839 ↗ splicing rna
      Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium.
      The International Cancer of the Pancreas Screening Consortium met in 2018 to update its consensus recommendations for the management of individuals with increased risk of pancreatic cancer based on family history or germline mutation status (high-risk individuals). A modified Delphi approach was employed to reach consensus among a multidisciplinary group of experts who voted on consensus statement
      BP7PP3PP5PS4PVS1
      11598466 ↗ case observation
      Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal cancer--supporting documentation.
      PP5PS4
      15604628 ↗ case observation
      Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Cancer Genetic Counseling Special Interest Group. The information contained in
      PP5PS4
      20301390 ↗ case observation
      Untitled reference
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PS3PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots