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PMS2
Final classification
Uncertain Significance - Conflicting Evidence
PMS2 c.33T>C · p.Pro11=
PMS2

NM_000535.7:c.33T>C (p.Pro11=) is a synonymous variant in exon 2 of PMS2. It is absent from gnomAD v4.1, meeting PM2_Supporting under the InSiGHT VCEP v2.0.0 framework (allele frequency < 0.00002).

Gene
PMS2
Transcript
NM_000535.7
HGVS · transcript:coding
NM_000535.7:c.33T>C
Consequence
N/A
GRCh38
chr7:6006022 A>G
GRCh37
chr7:6045653 A>G
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.33T>C

NM_000535.7:c.33T>C (p.Pro11=) is a synonymous variant in exon 2 of PMS2. It is absent from gnomAD v4.1, meeting PM2_Supporting under the InSiGHT VCEP v2.0.0 framework (allele frequency < 0.00002).1 SpliceAI predicts no splicing impact for this synonymous variant (max delta score = 0.00, ≤ 0.1), meeting BP4_Supporting under the InSiGHT VCEP v2.0.0 framework.2 ClinVar records this variant as Likely benign (4 submissions from clinical laboratories; ClinVar Variation ID 525878), though the review status is criteria provided, single submitter and this alone does not constitute an independent ACMG criterion under the VCEP framework.3 No functional studies, segregation data, tumor phenotype data, or variant-specific literature were identified for NM_000535.7:c.33T>C. Multiple criteria (PS3, BS3, PP1, PP4, BS4, BP5) could not be assessed due to absence of evidence. Applying the InSiGHT MMR VCEP v2.0.0 combination rules: PM2_Supporting (pathogenic supporting) and BP4_Supporting (benign supporting) are both met. With one pathogenic supporting and one benign supporting criterion and no criteria at higher strength levels, the combination rules do not yield a definitive classification. This results in a classification of Uncertain Significance.4

PM2 + BP4 Uncertain Significance - Conflicting Evidence
Gene diagram · NM_000535.7 · variants mapped to exon structure
PMS2 NM_000535.7
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000535.7:c.33T>C is absent from gnomAD v4.1 (0 alleles), meeting the InSiGHT VCEP PM2_Supporting threshold of allele frequency < 0.00002 (<1 in 50,000 alleles).
Absent from gnomAD v4.1 (0/1614074 alleles
BP4 supporting Benign
NM_000535.7:c.33T>C is a synonymous variant and SpliceAI predicts no splicing impact (max delta score = 0.00, which is ≤ 0.1), meeting the InSiGHT VCEP BP4_Supporting threshold for intronic and synonymous variants.
SpliceAI max delta score = 0.00. Synonymous variant with no predicted effect on splicing.
Assessed · not applied
Pathogenic
PS2 No de novo observations reported for NM_000535.7:c.33T>C.
PS3 No calibrated functional assay data or MMR functional assay results are available for NM_000535.7:c.33T>C.
PP1 No co-segregation data are available for NM_000535.7:c.33T>C.
PP3 PP3 under the InSiGHT VCEP requires either a missense variant with HCI prior probability > 0.68, or a predicted splice defect at non-canonical splice nucleotides with SpliceAI delta ≥ 0.2.
PP4 No tumor MSI/IHC data are available for patients carrying NM_000535.7:c.33T>C.
Benign
BA1 BA1 requires gnomAD v4 Grpmax filtering allele frequency ≥ 0.0028 (0.28%).
BS1 BS1 requires gnomAD v4 Grpmax filtering allele frequency ≥ 0.00028 and < 0.0028.
BS2 BS2 requires co-occurrence in trans with a known pathogenic PMS2 variant in a patient with colorectal cancer after age 45 without CMMRD.
BS3 No calibrated functional assay data demonstrating proficient MMR function are available for NM_000535.7:c.33T>C.
BS4 No segregation data are available to assess lack of co-segregation with disease for NM_000535.7:c.33T>C.
BP5 No tumor MSS/IHC data are available for patients carrying NM_000535.7:c.33T>C.
BP7 BP7 requires a synonymous variant at or within -21/+7 of the exon-intron boundaries (splice consensus region).
N/A · 11 PVS1 · PS1 · PS4 · PM1 · PM5 · 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
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 Likely benign (2 clinical laboratories) and as Likely Benign (1 clinical laboratory) and as Benign (1 clinical laboratory). (ClinVarID = 525878)
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.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
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
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
25711197 ↗ Lynch Syndrome: A Primer for Urologists and Panel Recommendations. CLINVAR
26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
34012068 ↗ 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). CLINVAR
34043773 ↗ European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR