PTEN c.765_801+20delinsC, p.?

Reasoning

The NM_000314.8 delins begins in exon 7 at c.765 and extends through c.801+20, deleting the terminal coding portion of the exon and the intron-7 donor site. SpliceAI predicts near-complete donor loss (DS_DL 0.999). PTEN loss of function is an established disease mechanism, and the PTEN Expert Panel PVS1 decision tree assigns PVS1 to disruption at or 5′ of p.D375 in NM_000314.8 when the resulting aberrant splicing disrupts the reading frame and is predicted to undergo NMD. This disruption is well upstream of c.1121/p.D375; deletion of exon 7 (37 coding bases) would be out of frame. PVS1 is therefore met at Very Strong strength, contingent on the predicted out-of-frame/NMD consequence.

Rule

PTEN Expert Panel PVS1 decision tree: canonical GT-AG splice-site disruption at or 5′ of p.D375/c.1121 in NM_000314.8, with out-of-frame aberrant splicing predicted to undergo NMD, is assigned PVS1.

Evidence considered

• VariantValidator maps NM_000314.8:c.765_801+20delinsC from exon 7 into intron 7; the deleted interval includes the c.801 donor boundary and extends 20 intronic bases.
• SpliceAI reports DS_DL 0.999 (donor loss) for this variant.
• The PTEN Expert Panel decision tree uses NM_000314.8 and assigns PVS1 to a splice disruption at or 5′ of c.1121/p.D375 when aberrant splicing disrupts the reading frame and is predicted to undergo NMD.

Still missing

• No RNA or other splice assay is available to confirm the actual aberrant transcript and NMD for this complex exon/intron delins.
• Because the variant deletes both exonic sequence and the canonical donor rather than being an isolated ±1/2 substitution, confirm exon definition and the predicted splice product during clinical review.

Sources

Reasoning

PM2 Supporting is met under the PTEN Expert Panel Version 3.2 specification. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, satisfying the specified population-absence requirement of <0.00001 (0.001%) allele frequency; no subpopulation allele observations were reported.

Rule

Absent in population; databases present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. If multiple alleles are present within any subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%).

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies PM2 at Supporting strength for variants absent in gnomAD or another large sequenced population, with allele frequency <0.00001 (0.001%); if multiple alleles are present within a subpopulation, that subpopulation frequency must be <0.00002 (0.002%).
• The case evidence reports the variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no population or subpopulation allele count detected.

Sources

Reasoning

PM4 is not met. The PTEN Expert Panel restricts PM4 for in-frame insertions/deletions to those affecting at least one residue in a defined catalytic motif, or to protein-extension variants. This exon/intron delins has no established in-frame protein consequence (p.?) and is evaluated as a splice-disrupting predicted loss-of-function variant rather than an in-frame protein-length change. It is not a stop-loss/protein-extension variant.

Rule

PTEN Expert Panel PM4: in-frame insertions/deletions must affect at least one catalytic-motif residue specified for PM1; protein-extension variants also qualify.

Evidence considered

• The normalized protein consequence is NP_000305.3:p.?, so no in-frame protein length change has been established.
• The PTEN Expert Panel permits PM4 only for in-frame insertions/deletions affecting at least one PM1 catalytic-motif residue, or for variants resulting in protein extension.

Sources

Reasoning

BA1 is not met. The variant was reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore its allele frequency does not exceed the PTEN Expert Panel stand-alone benign threshold of >0.00056 (0.056%).

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• The PTEN Expert Panel Version 3.2 rule specifies BA1 at a gnomAD filtering allele frequency >0.00056 (0.056%).
• The case evidence reports this variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no allele-frequency observation available.

Sources

Reasoning

BS1 is not met. The variant was reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no population allele frequency reaches the PTEN Expert Panel BS1 ranges of 0.0000043 to <0.00056.

Rule

Strong: gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%); Supporting: allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies BS1 Strong for gnomAD filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%), and BS1 Supporting from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
• The case evidence reports absence of the variant from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; no allele frequency or ancestry-specific frequency was identified.

Sources

Reasoning

BP4 requires SpliceAI and VarSeak to predict no splicing impact; PTEN defines a benign SpliceAI range of 0–0.2. The observed SpliceAI maximum delta score is 0.999, which is incompatible with BP4 regardless of the unavailable VarSeak result.

Rule

PTEN EP BP4: for splice-region variants, SpliceAI and VarSeak must both predict no splicing impact; SpliceAI 0–0.2 is benign evidence.

Evidence considered

• PTEN Expert Panel BP4 for synonymous or intronic variants requires both SpliceAI and VarSeak to predict no impact; SpliceAI scores 0–0.2 are considered benign evidence and VarSeak classes 1–2 are considered benign evidence.
• SpliceAI for NM_000314.8:c.765_801+20delinsC reported a maximum delta score of 0.999, with predicted donor loss DS_DL 0.999.

Sources

Reasoning

The PTEN Expert Panel specification is applicable, but the case bundle contains no proband-level clinical description, parental testing, maternity/paternity confirmation, family history, or de novo observation for this variant. Therefore PS2 cannot be assessed.

Rule

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

Evidence considered

• ClinGen PTEN Expert Panel Specification v3.2 defines PS2 as applicable for a de novo observation in an affected patient with no family history, with both maternity and paternity confirmed for PS2_Strong; the case bundle provides none of these case-level observations.
• The case bundle reports no literature PMIDs or paper extracts and contains no segregation or parental-testing data for NM_000314.8:c.765_801+20delinsC.

Still missing

• Documented affected proband with phenotype consistent with PTEN hamartoma tumor syndrome
• Variant absent in both biological parents
• Confirmation of both maternity and paternity
• No relevant family history

Sources

Reasoning

The ClinGen PTEN Expert Panel specification permits PS3 for an RNA, mini-gene, or other assay showing splice impact, and permits PS3_Moderate for PTEN phosphatase activity <= -1.11 per Mighell et al. 2018. The case bundle contains no variant-specific RNA, mini-gene, cellular, in vivo, or biochemical assay result. The variant is intronic (NM_000314.8:c.765_801+20delinsC; protein consequence p.?), so the PTEN missense saturation-mutagenesis table cannot be applied to this variant. SpliceAI prediction is computational evidence, not a validated functional assay, and does not establish PS3.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. RNA, mini-gene, or other assay shows impact on splicing.

Evidence considered

• The PTEN VCEP Version 3.2 rule states that PS3 Strong requires well-established in vitro or in vivo functional studies supportive of a damaging effect, including an RNA, mini-gene, or other assay showing impact on splicing.
• The PTEN VCEP Version 3.2 rule states that PS3 Moderate may be assigned for phosphatase activity <= -1.11 per Mighell et al. 2018 (PMID:29706350), while the local VCEP mmc2 resource is restricted to PTEN missense variants.
• The case bundle identifies NM_000314.8:c.765_801+20delinsC as an intronic variant with predicted protein consequence p.? and reports no variant-specific functional assay result.
• The case bundle reports SpliceAI max delta score 0.999; this is a computational prediction and cannot substitute for PS3 functional evidence.

Still missing

• Variant-specific RNA, mini-gene, or other validated splicing assay with appropriate controls is needed to assess PS3.
• No variant-specific biochemical, cellular, or in vivo functional assay result is available.
• No assay controls, replicate data, or quantitative calibration for this variant are available.

Sources

Reasoning

The PTEN Expert Panel PS4 specification requires either a sufficiently powered case-control result or phenotype-specific probands scored under its adult/pediatric system. No affected-proband observations, phenotype scores, or case-control data for this exact variant are present in the case evidence bundle.

Rule

PTEN VCEP PS4: case-control enrichment meeting the VCEP thresholds, or summed independent-proband phenotype-specificity score of at least 1.

Evidence considered

• PTEN VCEP PS4 permits case-control evidence only when a sufficiently powered study shows odds ratio >2 for a PHTS component phenotype, p<0.05, and a 95% confidence interval lower bound >1.5; alternatively it uses summed phenotype-specificity scores (supporting 1-1.5, moderate 2-3.5, strong 4-15.5, very strong >=16).
• The consolidated literature and case-evidence records contain no exact-variant publications, affected-proband phenotype data, specificity scores, or case-control counts.

Still missing

• Independent affected probands with complete PTEN phenotype data sufficient to calculate the VCEP specificity score, or a sufficiently powered case-control study for this exact variant.

Sources

Reasoning

The PTEN Expert Panel specification is applicable, but the case bundle contains no assumed de novo occurrence, affected proband information, parental testing results, or family-history assessment. Therefore PM6 cannot be assessed.

Rule

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

Evidence considered

• ClinGen PTEN Expert Panel Specification v3.2 defines PM6 for an assumed de novo variant without confirmed maternity and paternity in an affected proband with no family history; the case bundle contains no such observation.
• The case bundle reports no literature PMIDs or paper extracts and contains no proband, parental, or de novo evidence for NM_000314.8:c.765_801+20delinsC.

Still missing

• Documented affected proband with phenotype consistent with PTEN hamartoma tumor syndrome
• Evidence that the variant is absent in tested parents or otherwise presumed de novo
• Maternity and paternity confirmation status
• No relevant family history
• Number of independent presumed de novo observations

Sources

Reasoning

The PTEN Expert Panel specification requires co-segregation in multiple affected family members and at least 3 meioses for PP1 at supporting strength, with higher strengths requiring 5–6 or at least 7 meioses. The case bundle contains no family members, phenotypes, variant genotypes, phase information, or meiosis count. Therefore PP1 cannot be assessed.

Rule

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

Evidence considered

• ClinGen PTEN Expert Panel Specification v3.2 requires 3 or 4 meioses for PP1, 5 or 6 meioses for PP1_Moderate, and at least 7 meioses across at least two families for PP1_Strong.
• No segregation data, family history, affected relatives, or meiosis count is present in the case bundle.

Still missing

• Affected relatives with phenotype consistent with PTEN hamartoma tumor syndrome
• Variant testing results for affected relatives
• Informative family relationships and phase
• Count of informative meioses
• Evidence spanning the required number of families for PP1_Strong

Sources

Reasoning

The PTEN Expert Panel requires concordant SpliceAI and VarSeak predictions for splice-impact PP3. SpliceAI predicts a high splice impact (maximum delta score 0.999, including donor loss 0.999), but no VarSeak result is available; therefore the required concordance cannot be established.

Rule

PTEN EP PP3: Splicing variants require concordance of SpliceAI and VarSeak.

Evidence considered

• PTEN Expert Panel PP3 applies at supporting strength to splicing variants only with concordance of SpliceAI and VarSeak.
• SpliceAI for NM_000314.8:c.765_801+20delinsC reported DS_DL 0.999, DS_DG 0.633, DS_AL 0.465, DS_AG 0.069, and maximum delta score 0.999.

Still missing

• VarSeak classification for NM_000314.8:c.765_801+20delinsC is needed to determine whether the PTEN Expert Panel PP3 concordance requirement is met.

Sources

Reasoning

BS2 cannot be assessed from the available evidence. The population resources report the variant as absent, but provide no homozygote observations or clinical information about healthy or PHTS-unaffected individuals.

Rule

Observed in the homozygous state in a healthy or PHTS-unaffected individual. One observation if homozygous status confirmed, two if not confirmed. Apply at supporting level if BS1 is also applied.

Evidence considered

• The PTEN Expert Panel requires an observation in the homozygous state in a healthy or PHTS-unaffected individual; one observation is sufficient when homozygous status is confirmed, while two are required when it is not confirmed.
• The available gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada results are absent records and contain no homozygote or individual-level clinical evidence.

Still missing

• No confirmed homozygous observation in a healthy or PHTS-unaffected individual was provided.
• No two independent unconfirmed homozygous observations were provided.

Sources

Reasoning

The ClinGen PTEN Expert Panel specification requires well-established functional evidence showing no damaging effect for BS3 Strong, and allows BS3 Supporting for a functional study showing no damaging effect or phosphatase activity > 0 per Mighell et al. 2018. The case bundle contains no variant-specific negative functional result, normal splicing assay, or validated benign assay with appropriate controls. The intronic variant cannot be evaluated using the PTEN missense saturation-mutagenesis table, and the available SpliceAI prediction is not functional evidence. BS3 is therefore not assessed.

Rule

Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. To be applied to intronic or synonymous variants, RNA, mini-gene or other splicing assay demonstrating no splicing impact.

Evidence considered

• The PTEN VCEP Version 3.2 rule states that BS3 Strong requires well-established in vitro or in vivo functional studies showing no damaging effect and specifically allows RNA, mini-gene, or other splicing assay evidence demonstrating no splicing impact for intronic variants.
• The PTEN VCEP Version 3.2 rule states that BS3 Supporting may be assigned for a functional study showing no damaging effect or phosphatase activity > 0 per Mighell et al. 2018 (PMID:29706350), while the local VCEP mmc2 resource is restricted to PTEN missense variants.
• The case bundle identifies NM_000314.8:c.765_801+20delinsC as an intronic variant and contains no variant-specific functional assay result demonstrating preserved splicing or protein function.
• The case bundle reports SpliceAI max delta score 0.999; this computational prediction cannot establish BS3 or demonstrate normal function.

Still missing

• Variant-specific RNA, mini-gene, or other validated splicing assay demonstrating no splicing impact is needed to assess BS3.
• No variant-specific biochemical, cellular, or in vivo assay demonstrating preserved function is available.
• No assay controls, replicate data, or quantitative benign calibration for this variant are available.

Sources

Reasoning

The PTEN Expert Panel specification permits BS4 when the variant fails to segregate with disease in affected members of one family at supporting strength or two or more families at strong strength. The case bundle contains no affected-family genotypes, phenotypes, or non-segregation observations. Therefore BS4 cannot be assessed.

Rule

Lack of segregation in affected members of one family.

Evidence considered

• ClinGen PTEN Expert Panel Specification v3.2 defines BS4_Strong as lack of segregation in affected members of two or more families and BS4_Supporting as lack of segregation in one family.
• No non-segregation or affected-family data is present in the case bundle.

Still missing

• Affected family members evaluated for the variant
• Genotypes and phenotype status for each informative relative
• Documented lack of segregation in one or more families
• Assessment of phenocopies or multiple pathogenic variants as potential confounders

Sources

Reasoning

The PTEN-specific BP2 rule requires the variant to be observed in trans with a pathogenic or likely pathogenic PTEN variant, or to have at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants. The consolidated case-evidence bundle contains no affected-proband, co-occurring-variant, phase, cis/trans, or inheritance observations for this variant, so BP2 cannot be assessed.

Rule

BP2 Supporting: 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 ClinGen PTEN Expert Panel specifications, version 3.2, define BP2 at Supporting strength as either observation in trans with a pathogenic or likely pathogenic PTEN variant, or at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants.
• The case-evidence bundle reports no literature PMIDs and contains no affected-proband or allelic-phase observations for NM_000314.8:c.765_801+20delinsC.

Still missing

• No case-level observations identify a pathogenic or likely pathogenic PTEN variant in trans.
• No case-level observations document three or more cis or phase-unknown observations with different pathogenic or likely pathogenic PTEN variants.
• No family or proband data are available to establish phase or inheritance.

Sources

Reasoning

The PTEN Expert Panel requires at least two cases with a highly penetrant alternate molecular diagnosis and personal/family histories demonstrating no overlap between that disorder and PTEN. No such cases or alternate molecular diagnoses are present in the case evidence bundle.

Rule

PTEN VCEP BP5 Supporting: at least two qualifying alternate-diagnosis cases with no phenotype overlap with PTEN.

Evidence considered

• PTEN VCEP BP5 requires at least two cases; the alternate gene/disorder must be highly penetrant and the patient's personal/family history must demonstrate no overlap between that disorder and PTEN.
• No affected-case records or alternate molecular diagnoses for this exact variant are supplied in the consolidated evidence bundle.

Still missing

• At least two independent cases carrying this exact variant with a highly penetrant alternate molecular diagnosis and documented personal/family histories showing no phenotype overlap with PTEN.

Sources