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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 applied · 14 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
PM2_Supporting is met: NM_000535.7:c.14A>T is extremely rare in gnomAD v4.1 (AF=4.96e-06, 8/1,612,464 alleles, grpmax FAF=2.92e-06), which falls below the VCEP threshold of <0.00002 (<1 in 50,000 alleles). The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0.
gnomAD v4.1: 8/1612464 alleles (AF=4.96e-06
BP4 supporting Benign
BP4_Supporting is met: the HCI prior probability for pathogenicity is 0.004, which falls below the VCEP threshold of <0.11 for BP4_Supporting. Multiple in silico predictors support a benign effect: REVEL score 0.498 (below typical pathogenic threshold), BayesDel score 0.008 (strongly benign), and SpliceAI delta 0.00 (no splicing impact).
HCI prior = 0.004 (<0.11). REVEL = 0.498. BayesDel = 0.008. SpliceAI max delta = 0.00.
Assessed · not applied
Pathogenic
PS1 PS1 is not met: no different nucleotide change at Glu5 encoding the same Val substitution has been previously classified as Pathogenic by the InSiGHT/ClinGen VCEP for PMS2.
PS2 PS2 is not assessed: no de novo observation data for this variant were identified in ClinVar submissions, literature, or any supporting databases.
PS3 PS3 is not met: no variant-specific functional assay data are available for NM_000535.7:c.14A>T (p.Glu5Val).
PM5 PM5 is not met: no different missense variant at PMS2 residue Glu5 has been classified as Pathogenic or Likely Pathogenic by the VCEP.
PP1 PP1 is not met: no co-segregation data (Bayes Likelihood Ratio) are available for NM_000535.7:c.14A>T in any pedigree.
PP3 PP3 is not met: the HCI prior probability for pathogenicity is 0.004, which is far below both the VCEP Moderate threshold (>0.81) and the Supporting threshold (>0.68 and ≤0.81).
PP4 PP4 is not assessed: no tumor MSI/IHC data (MSI-H status, MMR protein expression) are available for patients carrying NM_000535.7:c.14A>T.
Benign
BA1 BA1 is not met: the gnomAD v4.1 grpmax filtering allele frequency is 2.92e-06, far below the VCEP stand-alone benign threshold of ≥0.0028 (0.28%).
BS1 BS1 is not met: the gnomAD v4.1 grpmax filtering allele frequency is 2.92e-06, far below the VCEP strong benign threshold of ≥0.00028 (0.028%).
BS2 BS2 is not met: no evidence of this variant occurring in trans with a known pathogenic PMS2 variant in a CRC patient over age 45 without CMMRD features.
BS3 BS3 is not met: no calibrated functional assay data are available for NM_000535.7:c.14A>T.
BS4 BS4 is not met: no co-segregation data (lack of segregation with disease) are available for this variant.
BP5 BP5 is not met: no tumor data demonstrating MSS status, intact MMR protein expression, or BRAF V600E/MLH1 methylation in carriers of this variant are available.
BP7 BP7 is not met: this criterion applies only to synonymous (silent) or intronic variants at or beyond positions -21/+7.
N/A · 9 PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP6
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= 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.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0005% · 8 / 1,612,464
0 hom · FAF 0.00029%
European (non-Finnish)
8 / 1,179,840
0.00068%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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.
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
24362816 ↗ Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. ONCOKB
25070057 ↗ Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer. CLINVAR
25645574 ↗ ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes. 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
31672839 ↗ Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium. CLINVAR
11598466 ↗ Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal cancer--supporting documentation. CLINVAR
15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
20301390 ↗ Lynch Syndrome. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR