PTEN c.-491_-486dup, p.?

Reasoning

Met at the PTEN-specific stand-alone level: the ClinGen PTEN Expert Panel Version 3.2 specifies BA1 for gnomAD filtering allele frequency >0.00056. The default all-comers gnomAD datasets apply because the specification does not require a non-cancer or exome-only subset. The variant's gnomAD v4.1 all-comers allele frequency is 0.0013939683 (526/377340), with a maximum population allele frequency of 0.006070159 in the Finnish population and grpmax FAF 0.00127765; gnomAD v2.1 also reports AF 0.0019932230 and grpmax FAF 0.00134244. These values exceed the PTEN BA1 threshold.

Rule

PTEN VCEP BA1 stand-alone: gnomAD filtering allele frequency >0.00056.

Evidence considered

• PTEN VCEP Version 3.2 specifies BA1 when gnomAD filtering allele frequency is >0.00056.
• The default all-comers gnomAD source is appropriate because the PTEN specification does not mandate a non-cancer or exome-only population subset.
• gnomAD v4.1 reports AF 0.0013939683 (526/377340), Finnish population AF 0.006070159, and grpmax FAF 0.00127765.
• gnomAD v2.1 reports AF 0.0019932230 and grpmax FAF 0.00134244.

Sources

Reasoning

Met at supporting strength under the PTEN-specific rule: BS2 supporting is met by two homozygous observations when clinical data are not provided. The default all-comers gnomAD v4.1 record reports three homozygotes overall, including two in the Finnish population and one in the European non-Finnish population. The record does not provide individual health or PHTS status, so the VCEP's no-clinical-data supporting level is used. gnomAD v2.1 reports no homozygotes, but does not negate the later v4.1 observations.

Rule

PTEN VCEP BS2 supporting: two homozygous observations with no clinical data provided; BS2 is not upgraded to strong without confirmed healthy or PHTS-unaffected status.

Evidence considered

• PTEN VCEP Version 3.2 specifies BS2 strong for one confirmed homozygous observation or two unconfirmed observations, and supporting for two homozygous observations without clinical data.
• gnomAD v4.1 reports three homozygotes overall: two in the Finnish population and one in the European non-Finnish population.
• The gnomAD record provides no individual clinical or PHTS-unaffected status, so the VCEP supporting rule for homozygous observations without clinical data applies.
• gnomAD v2.1 reports zero homozygotes.

Sources

Reasoning

Not met: the PTEN VCEP Version 3.2 requires allele frequency <0.00001 in gnomAD or another large sequenced population, and <0.00002 in any subpopulation when multiple alleles are present. The default all-comers gnomAD v4.1 AF is 0.0013939683, with Finnish AF 0.006070159 and grpmax FAF 0.00127765; gnomAD v2.1 likewise reports AF 0.0019932230 and grpmax FAF 0.00134244. The variant is therefore far above the PTEN PM2 threshold.

Rule

PTEN VCEP PM2 supporting: allele frequency <0.00001, or <0.00002 in any subpopulation when multiple alleles are present.

Evidence considered

• PTEN VCEP Version 3.2 defines PM2 supporting as allele frequency <0.00001 in gnomAD or another large sequenced population; if multiple alleles are present within a subpopulation, that subpopulation must be <0.00002.
• The default all-comers gnomAD v4.1 AF is 0.0013939683, with Finnish AF 0.006070159 and grpmax FAF 0.00127765.
• The default all-comers gnomAD v2.1 AF is 0.0019932230 with grpmax FAF 0.00134244.

Sources

Reasoning

PM4 is not met. The PTEN VCEP specification permits PM4 for in-frame insertions or deletions only when they affect at least one residue in a defined catalytic motif, or for variants causing protein extension. This variant lies upstream of the coding sequence in a normalized GGC repeat, has predicted protein consequence NP_000305.3:p.(=), and changes neither protein length nor a catalytic motif.

Rule

PTEN VCEP PM4: in-frame insertion/deletion must affect a catalytic motif, or the variant must cause protein extension.

Evidence considered

• The PTEN VCEP PM4 rule requires an in-frame insertion/deletion affecting at least one catalytic-motif residue or a protein extension; it does not support a 5' UTR repeat with unchanged protein consequence.
• Normalization gives NM_000314.8:c.-500_-486GGC[7] and NP_000305.3:p.(=); the variant is outside the coding sequence and does not alter protein length.

Sources

Reasoning

Not met under the PTEN-specific rule: BS1 strong requires gnomAD filtering allele frequency from 0.000043 through 0.00056, while BS1 supporting requires 0.0000043 through 0.000043. The default all-comers gnomAD v4.1 AF is 0.0013939683 and grpmax FAF is 0.00127765, both above the BS1 range and instead meeting PTEN BA1. gnomAD v2.1 is likewise above the BS1 range with AF 0.0019932230 and grpmax FAF 0.00134244.

Rule

PTEN VCEP BS1 strong: 0.000043 <= gnomAD filtering allele frequency <= 0.00056; supporting: 0.0000043 <= frequency <= 0.000043.

Evidence considered

• PTEN VCEP Version 3.2 defines BS1 strong as 0.000043 through 0.00056 and BS1 supporting as 0.0000043 through 0.000043.
• The default all-comers gnomAD v4.1 AF is 0.0013939683 with grpmax FAF 0.00127765, exceeding the PTEN BS1 range.
• The default all-comers gnomAD v2.1 AF is 0.0019932230 with grpmax FAF 0.00134244, also exceeding the PTEN BS1 range.

Sources

Reasoning

The PTEN VCEP permits BP2 at supporting strength when the variant is observed in trans with a pathogenic or likely pathogenic PTEN variant, or when there are at least three observations in cis or phase unknown with different pathogenic or likely pathogenic PTEN variants. The available case evidence documents no affected-proband observation, parental or offspring phase result, trans/cis relationship, or qualifying co-occurrence with another pathogenic or likely pathogenic PTEN variant. ClinVar records classification submissions but no phase or allelic co-occurrence data. Therefore BP2 is not met.

Rule

Observed in trans with a pathogenic or likely pathogenic PTEN variant OR at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants.

Evidence considered

• The PTEN VCEP BP2 rule requires either one trans observation with a pathogenic or likely pathogenic PTEN variant or at least three cis/phase-unknown observations with different pathogenic or likely pathogenic PTEN variants.
• The case evidence contains no affected-proband, family, parental, offspring, or laboratory phase observation establishing trans or cis status with another pathogenic or likely pathogenic PTEN variant.
• ClinVar variation 492721 reports classification submissions but does not provide qualifying allelic phase or co-occurrence observations.

Still missing

• No documented affected-proband or family-level phase data identify this variant in trans with a pathogenic or likely pathogenic PTEN variant.
• No three independent cis or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants are documented.

Sources

Reasoning

No case-level proband report documents this variant as de novo, and no parental testing establishes both maternity and paternity. The PTEN VCEP PS2 rule requires a de novo observation in a patient with the disease and no family history, with both maternity and paternity confirmed for PS2 Strong; the required clinical and parental evidence is absent.

Rule

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history.

Evidence considered

• The governing PTEN Expert Panel specification requires confirmed maternity and paternity for PS2 Strong and requires the patient to have the disease with no family history.
• The case-evidence materials contain no variant-specific proband, parental-testing, or de novo observation supporting this criterion.

Still missing

• A clinical proband carrying NM_000314.8:c.-491_-486dup with a documented PTEN hamartoma tumor syndrome phenotype has not been identified.
• Maternal and paternal identity and variant-negative parental testing are not documented.
• Family history and absence of disease in relatives are not documented.

Sources

Reasoning

The PTEN VCEP specifies PS3_Moderate from Mighell et al. 2018 Table S2 only when the variant is listed in the missense assay table with High_conf=TRUE and Cum_score <= -1.11, and PS3_Supporting for qualifying functional assays below that threshold. The governing mmc2.xlsx full-text table contains no entry for c.-491_-486dup, p.?, or p.(=); the normalized variant is a 5' UTR duplication predicted to preserve the protein (p.(=)), not a missense variant represented in this assay. No variant-specific validated functional or splicing assay evidence is available in the reviewed case materials, so PS3 cannot be assigned.

Rule

PS3_Moderate requires Mighell et al. 2018 Table S2 High_conf=TRUE and Cum_score <= -1.11; PS3_Supporting requires qualifying functional evidence that does not meet PS3_Moderate.

Evidence considered

• ClinGen PTEN VCEP v3.2 specifies PS3_Moderate for Mighell et al. 2018 Table S2 variants with High_conf=TRUE and Cum_score <= -1.11, and PS3_Supporting for qualifying functional studies that do not meet the moderate threshold.
• The normalized case evidence identifies NM_000314.8:c.-491_-486dup as a 5' UTR duplication with predicted protein consequence NP_000305.3:p.(=), not a missense substitution.
• Direct searches of the complete governing mmc2.xlsx text for c.-491_-486dup, p.?, and p.(=) found no variant entry; therefore no Cum_score, High_conf flag, or assay result can be applied.

Still missing

• No entry for c.-491_-486dup was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No entry for p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No entry for p.(=) was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• A variant-specific RNA, mini-gene, or other validated functional assay assessing this 5' UTR duplication would be needed to assess PS3.

Sources

Reasoning

The PTEN Expert Panel specification permits PS4 for a sufficiently powered case-control study only when the odds ratio is >2, p<0.05, and the 95% confidence interval lower limit is >1.5; it also permits phenotype-specific scoring: 1 point per adult proband with Cleveland Clinic score >=30, 0.5 points for scores 25-29, 1 point per child with pediatric phenotype score >=5, or 0.5 points for score 4 subject to the stated exclusions. Strength is Very Strong for a specificity score >=16, Strong for 4-15.5 or qualifying case-control enrichment, Moderate for 2-3.5, and Supporting for 1-1.5. The available evidence contains no case-control odds ratio, p value, confidence interval, phenotype-specific score, or qualifying proband-level clinical data for this exact variant. The variant is present in gnomAD v4.1 at AF 0.00139397, which is population data rather than PS4 case-control enrichment. The exact numeric comparison cannot be performed because no PS4 value is available: OR >2, p<0.05, and 95% CI lower limit >1.5 are not assessable.

Rule

PTEN VCEP v3.2: case-control OR >2 with p<0.05 and 95% CI lower limit >1.5; alternatively specificity score >=16 for Very Strong, 4-15.5 for Strong, 2-3.5 for Moderate, or 1-1.5 for Supporting. PS4 may not be applied if BS1 applies.

Evidence considered

• PTEN VCEP v3.2 states that a sufficiently powered case-control study may support PS4 when odds ratio >2, p<0.05, and the 95% confidence interval lower limit >1.5.
• PTEN VCEP v3.2 assigns PS4 strength using aggregate phenotype-specific scores: Very Strong >=16, Strong 4-15.5, Moderate 2-3.5, and Supporting 1-1.5.
• gnomAD v4.1 reports the exact variant at allele frequency 0.00139397 (526/377340 alleles); this is population frequency evidence and does not provide PS4 case-control enrichment.

Still missing

• Exact-variant case-control data with odds ratio, p value, and 95% confidence interval are unavailable.
• Independent proband-level Cleveland Clinic or pediatric phenotype scores are unavailable.

Sources

Reasoning

No assumed de novo observation is documented for a patient with PTEN hamartoma tumor syndrome and no family history. The PTEN VCEP permits PM6 Moderate for one assumed de novo observation without confirmed maternity and paternity, PM6 Strong for two such probands or one highly specific phenotype, and PM6 Very Strong for the specified multiple-occurrence combinations; none can be evaluated from the available case evidence.

Rule

Assumed de novo, but without confirmation of paternity and maternity, in proband with the disease and no family history.

Evidence considered

• The governing PTEN Expert Panel specification defines PM6 Moderate as an assumed de novo occurrence in a patient with the disease and no family history without confirmed maternity and paternity.
• The case-evidence materials contain no variant-specific assumed de novo proband observations or phenotype and family-history documentation.

Still missing

• No variant-specific disease proband with an assumed de novo occurrence is documented.
• No information is available on maternity, paternity, or family history for any proband.
• No second proband or highly specific PTEN phenotype is documented for possible PM6 Strong application.

Sources

Reasoning

No affected relatives carrying the variant and no informative familial transmissions are documented. The PTEN VCEP requires co-segregation in multiple affected family members with 3 or 4 meioses for PP1 Supporting, 5 or 6 for PP1 Moderate, and at least 7 across at least two families for PP1 Strong; the available evidence establishes zero evaluable meioses.

Rule

Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed.

Evidence considered

• The governing PTEN Expert Panel specification requires 3 or 4 meioses with co-segregation in multiple affected family members for PP1 Supporting.
• The case-evidence materials contain no family segregation data, affected-relative genotypes, or meiosis count for this variant.

Still missing

• No family pedigree or affected relatives are documented.
• No genotype results for relatives are documented.
• No informative meioses or segregation counts are available.

Sources

Reasoning

The PTEN VCEP specifies BS3_Supporting from Mighell et al. 2018 Table S2 only when the variant is listed in the missense assay table with High_conf=TRUE and Cum_score > 0; BS3_Strong applies to qualifying evidence of no damaging effect on splicing for intronic or synonymous variants. The governing mmc2.xlsx full-text table contains no entry for c.-491_-486dup, p.?, or p.(=), and no variant-specific assay demonstrates preserved PTEN function or lack of splicing impact for this 5' UTR duplication. BS3 therefore cannot be assigned.

Rule

BS3_Supporting requires Mighell et al. 2018 Table S2 High_conf=TRUE and Cum_score > 0; BS3_Strong requires qualifying functional or splicing evidence showing no damaging effect.

Evidence considered

• ClinGen PTEN VCEP v3.2 specifies BS3_Supporting for Mighell et al. 2018 Table S2 variants with High_conf=TRUE and Cum_score > 0, and BS3_Strong for qualifying evidence showing no damaging effect on splicing where applicable.
• The normalized case evidence identifies NM_000314.8:c.-491_-486dup as a 5' UTR duplication with predicted protein consequence NP_000305.3:p.(=), not a missense substitution.
• Direct searches of the complete governing mmc2.xlsx text for c.-491_-486dup, p.?, and p.(=) found no variant entry; consequently no benign assay score or high-confidence flag is available.

Still missing

• No entry for c.-491_-486dup was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No entry for p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• No entry for p.(=) was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PTEN/fulltext/mmc2.xlsx.txt.
• A variant-specific RNA, mini-gene, or other validated assay showing no functional or splicing impact would be needed to assess BS3.

Sources

Reasoning

No affected family members carrying the variant are documented, so lack of segregation cannot be established. The PTEN VCEP permits BS4 Supporting for lack of segregation in one family and BS4 Strong for two or more families, but neither affected-family comparison is available.

Rule

Lack of segregation in affected members of one family.

Evidence considered

• The governing PTEN Expert Panel specification defines BS4 Supporting as lack of segregation in affected members of one family and BS4 Strong as lack of segregation in two or more families.
• The case-evidence materials contain no affected-family genotype and phenotype data establishing non-segregation.

Still missing

• No affected relatives with documented phenotype are identified.
• No relative genotypes are available to demonstrate presence or absence of the variant.
• The number of families with evaluable non-segregation evidence is unknown.

Sources

Reasoning

The PTEN Expert Panel permits BP5 at Supporting strength when the variant is found in a case with an alternate molecular basis for disease, but requires at least two such cases; the other gene/disorder must be highly penetrant and the patient's personal/family history must demonstrate no overlap with PTEN. The available case evidence contains no qualifying alternate-gene diagnoses, two-case series, or personal/family-history data for this exact variant. No BP5 numeric threshold is specified, so no numeric comparison is applicable.

Rule

PTEN VCEP v3.2 BP5 Supporting: variant found in a case with an alternate molecular basis for disease; at least two cases are required, the other gene/disorder must be highly penetrant, and personal/family history must show no overlap between the other gene and PTEN.

Evidence considered

• PTEN VCEP v3.2 requires at least two BP5 cases, a highly penetrant alternate gene/disorder, and personal/family history demonstrating no overlap with PTEN.
• No qualifying alternate molecular basis or corresponding clinical-history evidence is present for this exact variant.

Still missing

• At least two exact-variant cases with an alternate molecular basis are unavailable.
• Evidence that each alternate disorder is highly penetrant and has no phenotype overlap with PTEN is unavailable.

Sources