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PMS2
Final classification
Likely Benign
PMS2 c.2566C>T · p.Leu856=
PMS2

NM_000535.7:c.2566C>T (p.Leu856=) is a synonymous variant in exon 15 of PMS2. It is extremely rare in population databases, with an allele frequency of 5.057e-06 in gnomAD v4.1 (5/988,724 alleles, no homozygotes) and absent from gnomAD v2.1, satisfying PM2_Supporting per PMS2 VCEP v2.0.0.

Gene
PMS2
Transcript
NM_000535.7
HGVS · transcript:coding
NM_000535.7:c.2566C>T
Consequence
N/A
GRCh38
chr7:5973422 G>A
GRCh37
chr7:6013053 G>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 Rule19 (Benign.Supporting >=2) with applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; maps to Likely Benign.
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 Rule19 (Benign.Supporting >=2) with applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; maps to Likely Benign.
Classification rationale
PM2 BP4BP7 Likely Benign
PMS2 c.2566C>T

NM_000535.7:c.2566C>T (p.Leu856=) is a synonymous variant in exon 15 of PMS2. It is extremely rare in population databases, with an allele frequency of 5.057e-06 in gnomAD v4.1 (5/988,724 alleles, no homozygotes) and absent from gnomAD v2.1, satisfying PM2_Supporting per PMS2 VCEP v2.0.0.1 SpliceAI predicts no splicing impact for this variant (max delta = 0.00), satisfying BP4_Supporting per PMS2 VCEP v2.0.0 for synonymous variants.2 The variant is a synonymous substitution located at c.2566 in exon 15, +120 nucleotides from the splice acceptor site, well beyond the +7 position defined by the BP7 rule. BP7_Supporting is met per PMS2 VCEP v2.0.0.3 PVS1, PS1, and PM5 are not applicable as this is a synonymous variant producing no amino acid change. PS4, PM1, PM6, PP2, PP5, BP1, BP2, and BP6 are not applicable per the PMS2 VCEP v2.0.0 specifications.4 No de novo observations (PS2), functional studies (PS3, BS3), cosegregation data (PP1, BS4), trans co-occurrence data (BS2), tumor pathology data (PP4, BP5), or computational evidence supporting pathogenicity (PP3) were identified for this variant. This variant has been reported in ClinVar as Likely benign by four clinical laboratories and Benign by one clinical laboratory (ClinVar ID 701564). In ClinVar, submissions cited methodology papers without variant-specific clinical evidence.5 Under the PMS2 VCEP v2.0.0 combination rules, the presence of two benign supporting criteria (BP4_Supporting, BP7_Supporting) satisfies Rule19 (>=2 Benign.Supporting -> Likely Benign). PM2_Supporting is also met but does not alter the classification under the VCEP rule hierarchy.6

PM2 + BP4 + BP7 Likely Benign
Gene diagram · NM_000535.7 · variants mapped to exon structure
PMS2 NM_000535.7
Fetching transcript structure from UCSC…
Applied criteria · 3 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
      Population frequency
      Overall AF
      5 / 988,724
      0.00051%
      Highest · Remaining individuals
      0.0024%
      Homozygotes
      0
      grpmax FAF
      0.00014%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 4 / 671,666 0.0006% 0
      Admixed American 0 / 44,772
      European (Finnish) 0 / 52,332
      Amish 0 / 652
      East Asian 0 / 34,106
      Middle Eastern 0 / 3,322
      South Asian 0 / 70,350
      Ashkenazi Jewish 0 / 23,308
      African/African American 0 / 46,988
      This variant is present in gnomAD v4.1 (AF= 5.05702e-06; MAF= 0.00051%, 5/988724 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 2.42554e-05; MAF= 0.00243%, 1/41228 alleles, homozygotes = 0); grpmax FAF= 1.39e-06.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 701564)
      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.
      Literature · 10 PMIDs triaged · 8 high-priority
      10papers 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.
      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
      20301390 ↗ case observation
      Untitled reference
      PP5PS4
      23788249 ↗ case observation
      ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
      In clinical exome and genome sequencing, there is a potential for the recognition and reporting of incidental or secondary findings unrelated to the indication for ordering the sequencing but of medical value for patient care. The American College of Medical Genetics and Genomics (ACMG) recently published a policy statement on clinical sequencing that emphasized the importance of alerting the pati
      PP5PS4
      25356965 ↗ case observation
      ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.
      These recommendations are designed primarily as an educational resource for medical geneticists and other health-care providers to help them provide quality medical genetics services. Adherence to these recommendations does not necessarily ensure a successful medical outcome. These recommendations should not be considered inclusive of all proper procedures and tests or exclusive of other procedure
      PP5PS4
      25394175 ↗ case observation
      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.
      The practice guidelines of the American College of Medical Genetics and Genomics (ACMG) and the National Society of Genetic Counselors (NSGC) are developed by members of the ACMG and NSGC to assist medical geneticists, genetic counselors, and other health-care providers in making decisions about appropriate management of genetic concerns, including access to and/or delivery of services. Each pract
      PP5PS4
      27854360 ↗ case observation
      Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.
      Disclaimer: These recommendations are designed primarily as an educational resource for medical geneticists and other healthcare providers to help them provide quality medical services. Adherence to these recommendations is completely voluntary and does not necessarily assure a successful medical outcome. These recommendations should not be considered inclusive of all proper procedures and tests o
      PP5PS4
      34012068 ↗ case observation
      ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG).
      PP5PS4
      34043773 ↗ case observation
      European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender.
      Lynch syndrome is the most common genetic predisposition for hereditary cancer but remains underdiagnosed. Large prospective observational studies have recently increased understanding of the effectiveness of colonoscopic surveillance and the heterogeneity of cancer risk between genotypes. The need for gene- and gender-specific guidelines has been acknowledged. The European Hereditary Tumour Group
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots