PTEN c.488_492+5del, p.?

Reasoning

The ClinGen PTEN Expert Panel specifies PM2 Supporting when the variant is absent or has allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; if multiple alleles are present in a subpopulation, that subpopulation frequency must be <0.00002 (0.002%). The variant is absent from gnomAD v2.1, gnomAD v4.1, and the available non-cancer subsets, satisfying the PTEN PM2 rule.

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 specifies PM2 Supporting for allele frequency <0.00001 (0.001%) in gnomAD or another large sequenced population; where multiple alleles occur in a subpopulation, that frequency must be <0.00002 (0.002%).
• The variant search returned absent in GNOMAD_V2_1, GNOMAD_V4_1, GNOMAD_V2_1_NON_CANCER, and GNOMAD_V3_1_NON_CANCER, supporting an allele frequency of zero in each queried dataset.

Sources

Reasoning

The ClinGen PTEN Expert Panel specifies BA1 for a gnomAD filtering allele frequency >0.00056 (0.056%). The variant is absent from gnomAD v2.1, gnomAD v4.1, and the available non-cancer subsets, so no population frequency reaches the BA1 threshold.

Rule

gnomAD Filtering allele frequency >0.00056 (0.056%)

Evidence considered

• The PTEN Expert Panel Version 3.2 specifies BA1 at gnomAD filtering allele frequency >0.00056 (0.056%).
• The variant search returned absent in GNOMAD_V2_1, GNOMAD_V4_1, GNOMAD_V2_1_NON_CANCER, and GNOMAD_V3_1_NON_CANCER; therefore the observed allele frequency is not elevated above the BA1 threshold.

Sources

Reasoning

The ClinGen PTEN Expert Panel specifies BS1 Strong for a gnomAD filtering allele frequency from 0.000043 to 0.00056 and BS1 Supporting from 0.0000043 to 0.000043. The variant is absent from gnomAD v2.1, gnomAD v4.1, and the available non-cancer subsets, so neither frequency interval is met.

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 specifies BS1 Strong at allele frequency 0.000043-0.00056 and BS1 Supporting at 0.0000043-0.000043.
• The variant search returned absent in GNOMAD_V2_1, GNOMAD_V4_1, GNOMAD_V2_1_NON_CANCER, and GNOMAD_V3_1_NON_CANCER; no allele frequency falls within either BS1 interval.

Sources

Reasoning

The variant NM_000314.8:c.488_492+5del is an intronic splice-region variant, so BP4 must use the SpliceAI path rather than REVEL. SpliceAI reports a maximum delta score of 0.994, indicating predicted splice impact and exceeding both the generic BP4 supporting threshold of 0.1 and the PTEN VCEP requirement for no-impact computational evidence; therefore BP4 is not met.

Rule

PTEN VCEP Version 3.2 BP4 supporting: splicing variants require concordant no-impact evidence from SpliceAI and VarSeak.

Evidence considered

• The PTEN VCEP Version 3.2 BP4 rule requires computational evidence suggesting no impact; for splicing variants it specifies concordance of SpliceAI and VarSeak.
• SpliceAI reports a maximum delta score of 0.994, with DS_DL 0.994 as the highest component score.
• The supplied generic SpliceAI calibration identifies <=0.1 as the BP4 supporting threshold; 0.994 is above this threshold and is not benign splice-impact evidence.

Sources

Reasoning

The PTEN VCEP PVS1 decision tree was consulted in full and searched for c.488_492+5del, p.? and p.?; no variant-specific pre-assigned entry was found. The variant is NM_000314.8:c.488_492+5del, a noncanonical splice-region deletion extending through +5, with NP_000305.3:p.? and no experimentally established exon-skipping or cryptic-splice consequence, reading-frame effect, or NMD outcome. SpliceAI predicts splice impact (max delta 0.994), but this prediction alone does not establish the decision-tree branch requiring exon skipping or cryptic-splice use that disrupts the reading frame and undergoes NMD. Therefore PVS1 cannot be assigned from the available evidence without resolving the transcript consequence and NMD outcome.

Rule

PTEN VCEP PVS1 decision tree; apply only when the splice consequence, reading-frame effect, and NMD branch are established.

Evidence considered

• The PTEN CSPEC Version 3.2 states that PVS1 uses the PTEN PVS1 decision tree and identifies NM_000314.8 as the preferred biologically relevant transcript.
• The full PVS1_DecisionTree_PTEN text assigns PVS1 for GT-AG +1/+2 splice-site variants when exon skipping or cryptic-splice use disrupts the reading frame and is predicted to undergo NMD; it does not provide a pre-assigned entry for this variant.
• The case variant is NM_000314.8:c.488_492+5del with NP_000305.3:p.?; SpliceAI reports DS_DL 0.994 and maximum delta 0.994, indicating predicted splice impact but not the resulting transcript or NMD outcome.

Still missing

• No entry for c.488_492+5del, p.? or p.? was found when searching PVS1_DecisionTree_PTEN.pdf.txt.
• Experimental or validated transcript evidence establishing exon skipping or cryptic-splice use, reading-frame disruption, and NMD outcome is unavailable.

Sources

Reasoning

The PTEN VCEP permits PS1 for the same amino-acid change as an established pathogenic variant, or for a different variant at the same nucleotide position as a pathogenic splice variant when predicted splice impact is equal or greater. This variant is intronic (NM_000314.8:c.488_492+5del) with an unresolved protein consequence (p.?), and the available case evidence contains no established pathogenic same-amino-acid or same-position splice comparator. Therefore PS1 cannot be adjudicated from the available evidence.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR different variant at same nucleotide position as a pathogenic splicing variant, where in silico models predict impact equal to or greater than the known pathogenic variant.

Evidence considered

• The PTEN VCEP PS1 rule requires either the same amino-acid change as an established pathogenic variant or a different variant at the same nucleotide position as a pathogenic splice variant with equal or greater predicted impact.
• VariantValidator reports NM_000314.8:c.488_492+5del with predicted protein consequence NP_000305.3:p.?, so a same-amino-acid comparison cannot be made from this case evidence.
• No ClinVar record or literature PMID was identified for this variant or a qualifying PS1 comparator in the collected evidence.

Still missing

• An established pathogenic same-amino-acid variant or pathogenic splice variant at the same nucleotide position, with comparable splice-impact evidence, is not available.

Sources

Reasoning

The PTEN VCEP requires a de novo observation in an affected patient with no family history and confirmation of both maternity and paternity for PS2 at strong strength. The available case evidence contains no proband phenotype, parental testing, maternity/paternity confirmation, or family-history information, so PS2 cannot be assessed.

Rule

ClinGen PTEN Expert Panel Specification v3.2: PS2 strong requires de novo occurrence with both maternity and paternity confirmed in a patient with the disease and no family history; PS2 very strong requires two proven, four assumed, or one proven plus two assumed de novo observations.

Evidence considered

• The PTEN Expert Panel specification defines PS2 strong as a de novo observation in a patient with the disease and no family history, with both maternity and paternity confirmed.
• No case-level proband, parental-testing, maternity/paternity, or family-history evidence is present in the reviewed case materials.

Still missing

• Affected proband documentation and phenotype consistent with PTEN hamartoma tumor syndrome
• Variant testing results for both biological parents
• Confirmed maternity and paternity
• Family-history assessment showing no relevant family history

Sources

Reasoning

The ClinGen PTEN VCEP specifies PS3_Strong for an RNA, mini-gene, or other assay demonstrating abnormal splicing, and PS3_Moderate for a high-confidence Mighell et al. 2018 phosphatase-assay result with a Table S2 Cum_score <= -1.11. This variant is an intronic splice-region deletion with predicted protein consequence p.?; no RNA or minigene functional result is present in the case evidence. The governing mmc2.xlsx file was searched for c.488_492+5del, c.488_492, p.?, and related variant notation, but contains no entry for this intronic variant and is explicitly a missense assay table. Therefore, no validated damaging functional assay evidence is available to assign PS3.

Rule

PTEN VCEP PS3_Strong: RNA, mini-gene, or other assay demonstrates impact on splicing. PTEN VCEP PS3_Moderate: Mighell et al. 2018 Table S2 variant is high confidence and has Cum_score <= -1.11.

Evidence considered

• ClinGen PTEN VCEP Version 3.2 specifies PS3_Strong for RNA, mini-gene, or other assays demonstrating an impact on splicing.
• The same specification limits PS3_Moderate from Mighell et al. 2018 to a variant listed as high confidence in mmc2.xlsx Table S2 with cumulative phosphatase-assay score <= -1.11.
• The case normalization identifies NM_000314.8:c.488_492+5del as an intronic splice-region deletion with NP_000305.3:p.?, not a missense variant.
• Direct searches of the full mmc2.xlsx text for c.488_492+5del, c.488_492, p.?, and 488_492 found no matching variant entry; the file describes Table S2 as protein-level missense variants.

Still missing

• No variant-specific RNA, minigene, or other validated splicing assay result is available.
• mmc2.xlsx was searched for c.488_492+5del, c.488_492, p.?, and related notation; no entry was found, and the file is restricted to missense variants.

Sources

Reasoning

The PTEN Expert Panel permits PS4 from either a sufficiently powered case-control study or accumulated phenotype-specific proband scores. For case-control evidence, the governing text requires odds ratio >2, p<0.05, and a 95% confidence-interval lower limit >1.5; it also states that PS4 cannot be applied with BS1. For phenotype specificity, the framework assigns 1 point per adult with Cleveland Clinic score ≥30 or child with pediatric score ≥5, with half-points for the specified intermediate scores, and requires a total of at least 1 point for PS4 Supporting, 2–3.5 for PS4 Moderate, 4–15.5 for PS4, or ≥16 for PS4 Very Strong. This case contains no proband-level phenotype scores, independent proband count, or case-control enrichment statistics, so PS4 cannot be assigned.

Rule

PTEN VCEP PS4: case-control odds ratio >2, p<0.05, and 95% confidence-interval lower limit >1.5; alternatively phenotype specificity score 1–1.5 for Supporting, 2–3.5 for Moderate, 4–15.5 for Strong, or ≥16 for Very Strong. PS4 may not be applied with BS1.

Evidence considered

• The PTEN Expert Panel PS4 specification requires a case-control odds ratio >2 with p<0.05 and a 95% confidence-interval lower limit >1.5, or a qualifying aggregate phenotype-specific proband score.
• The available case evidence contains no proband specificity scores or case-control enrichment statistics for this exact variant.

Still missing

• Independent proband-level PTEN phenotype or family-history specificity scores are unavailable.
• No sufficiently powered case-control study results, odds ratio, p-value, or 95% confidence interval are available.

Sources

Reasoning

The PTEN VCEP requires an assumed de novo occurrence in an affected proband with no family history when maternity and paternity are not confirmed. The available case evidence provides no proband phenotype, parental results, de novo observation, or family-history information, so PM6 cannot be assessed.

Rule

ClinGen PTEN Expert Panel Specification v3.2: PM6 moderate requires an assumed de novo occurrence without confirmation of maternity and paternity in a proband with disease and no family history; PM6 strong requires two presumed de novo observations or one presumed observation in a highly specific phenotype; PM6 very strong requires two proven, four assumed, or one proven plus two assumed observations.

Evidence considered

• The PTEN Expert Panel specification defines PM6 as an assumed de novo occurrence without confirmed maternity and paternity in a proband with disease and no family history; strength depends on the number of proven or assumed observations and phenotype specificity.
• No case-level de novo, proband, parental, or family-history evidence is present in the reviewed case materials.

Still missing

• Affected proband documentation and phenotype consistent with PTEN hamartoma tumor syndrome
• Evidence that the variant is absent in the tested parents or otherwise presumed de novo
• Maternity and paternity status
• Family-history assessment showing no relevant family history
• Number of independent de novo observations

Sources

Reasoning

The PTEN VCEP requires co-segregation with disease in multiple affected family members and assigns supporting strength for 3 or 4 meioses, moderate strength for 5 or 6 meioses, and strong strength for at least 7 meioses across at least two families. The available case evidence contains no affected relatives, genotype-phenotype segregation observations, family structure, or meiosis count, so PP1 cannot be assessed.

Rule

ClinGen PTEN Expert Panel Specification v3.2: PP1 supporting requires co-segregation in multiple affected family members with 3 or 4 observed meioses; PP1 moderate requires 5 or 6; PP1 strong requires at least 7 across at least two families.

Evidence considered

• The PTEN Expert Panel specification requires 3 or 4 meioses for PP1 supporting, 5 or 6 meioses for PP1 moderate, and at least 7 meioses across at least two families for PP1 strong.
• No case-level segregation or meiosis data are present in the reviewed case materials.

Still missing

• Affected relatives with clinical phenotype documentation
• Variant-testing results for relevant relatives
• Pedigree or family structure sufficient to count informative meioses
• Total informative meioses and number of families

Sources

Reasoning

The variant NM_000314.8:c.488_492+5del is an intronic splice-region variant, so PP3 must use the SpliceAI path rather than REVEL. SpliceAI reports a maximum delta score of 0.994, which exceeds the generic PP3 moderate threshold of 0.5, but the governing PTEN VCEP specification requires concordance of SpliceAI and VarSeak for PP3. No VarSeak result is present, so the VCEP-specific requirement cannot be verified and PP3 is not assessed rather than assigned from SpliceAI alone.

Rule

PTEN VCEP Version 3.2 PP3 supporting: splice variants require concordance of SpliceAI and VarSeak.

Evidence considered

• The PTEN VCEP Version 3.2 PP3 rule specifies supporting evidence for splice variants only when SpliceAI and VarSeak are concordant.
• SpliceAI reports DS_AG 0.001, DS_AL 0.393, DS_DG 0.178, and DS_DL 0.994; the maximum delta is 0.994.
• The supplied generic SpliceAI calibration identifies 0.5 as the PP3 moderate threshold, but the governing PTEN VCEP specification takes precedence.
• No VarSeak result is available for this variant.

Still missing

• A VarSeak result for NM_000314.8:c.488_492+5del is needed to verify the PTEN VCEP concordance requirement for PP3.

Sources

Reasoning

The PTEN Expert Panel requires observation in the homozygous state in a healthy or PHTS-unaffected individual, with one confirmed observation or two observations when homozygous status is not confirmed. The available case evidence contains population absence results but no homozygote observation or clinical-status evidence for this variant.

Rule

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

Evidence considered

• The PTEN Expert Panel BS2 rule requires a homozygous observation in a healthy or PHTS-unaffected individual; one observation is sufficient if homozygosity is confirmed, otherwise two are required.
• The queried gnomAD datasets report the variant as absent and provide no homozygote observation or individual clinical-status evidence.

Still missing

• No documented homozygous observation for the variant in a healthy or PHTS-unaffected individual.
• No homozygote-specific population count or clinical-status data are available.

Sources

Reasoning

The ClinGen PTEN VCEP specifies BS3_Strong for an RNA, mini-gene, or other assay demonstrating no splicing impact in intronic or synonymous variants, and BS3_Supporting for a high-confidence Mighell et al. 2018 phosphatase-assay result with Cum_score > 0 or other qualifying protein-function studies. This variant is an intronic splice-region deletion with protein consequence p.?; no variant-specific benign RNA, minigene, or other functional study is present in the case evidence. The governing mmc2.xlsx file was searched for c.488_492+5del, c.488_492, p.?, and related variant notation, but contains no entry for this intronic variant and is explicitly a missense assay table. Therefore, no validated benign functional assay evidence is available to assign BS3.

Rule

PTEN VCEP BS3_Strong: for intronic or synonymous variants, RNA, mini-gene, or other assay demonstrates no impact on splicing. PTEN VCEP BS3_Supporting: Mighell et al. 2018 Table S2 variant is high confidence and has Cum_score > 0.

Evidence considered

• ClinGen PTEN VCEP Version 3.2 specifies BS3_Strong for an RNA, mini-gene, or other assay demonstrating no splicing impact for intronic or synonymous variants.
• The same specification limits BS3_Supporting from Mighell et al. 2018 to a variant listed as high confidence in mmc2.xlsx Table S2 with cumulative phosphatase-assay score > 0.
• The case normalization identifies NM_000314.8:c.488_492+5del as an intronic splice-region deletion with NP_000305.3:p.?, not a missense variant.
• Direct searches of the full mmc2.xlsx text for c.488_492+5del, c.488_492, p.?, and 488_492 found no matching variant entry; the file describes Table S2 as protein-level missense variants.

Still missing

• No variant-specific RNA, minigene, or other validated splicing assay demonstrating no splice impact is available.
• mmc2.xlsx was searched for c.488_492+5del, c.488_492, p.?, and related notation; no entry was found, and the file is restricted to missense variants.

Sources

Reasoning

The PTEN VCEP defines BS4 as lack of segregation in affected members of a family, with strong strength requiring two or more families and supporting strength requiring one family. The available case evidence contains no affected-family-member testing or non-segregation observations, so BS4 cannot be assessed.

Rule

ClinGen PTEN Expert Panel Specification v3.2: BS4 supporting requires lack of segregation in affected members of one family; BS4 strong requires lack of segregation in affected members of two or more families.

Evidence considered

• The 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 affected members of two or more families.
• No case-level affected-relative testing or non-segregation evidence is present in the reviewed case materials.

Still missing

• Affected family members with phenotype documentation
• Variant-testing results for affected family members
• Pedigree or family structure linking tested individuals
• Number of families showing lack of segregation

Sources

Reasoning

The PTEN VCEP Version 3.2 specifies 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 and/or with phase unknown involving different pathogenic or likely pathogenic PTEN variants. The available case evidence contains no affected-proband observations, second PTEN variant, phase determination, cis/trans result, or qualifying multi-observation series. BP2 therefore cannot be assessed from the available evidence.

Rule

PTEN VCEP Version 3.2 BP2 supporting 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 or likely pathogenic PTEN variants.

Evidence considered

• The governing PTEN VCEP Version 3.2 defines BP2 as supporting when the variant is observed in trans with a pathogenic or likely pathogenic PTEN variant, or in at least three observations in cis and/or phase unknown with different pathogenic or likely pathogenic PTEN variants.
• The case evidence reports no affected-proband allelic observations, second PTEN variant, or phase information for this variant.

Still missing

• Affected-proband records with a second PTEN variant are unavailable.
• No cis/trans or phase-unknown relationship to a pathogenic or likely pathogenic PTEN variant is documented.
• No qualifying series of at least three observations with different pathogenic or likely pathogenic PTEN variants is documented.

Sources

Reasoning

The PTEN Expert Panel allows BP5 at Supporting strength only when the variant is found in at least two cases with an alternate molecular basis for disease, the alternate gene or disorder is highly penetrant, and the patients' personal or family histories show no overlap with PTEN. The available case evidence provides no such two-case series, alternate molecular diagnoses, penetrance documentation, or non-overlapping phenotype histories, so BP5 cannot be assessed.

Rule

PTEN VCEP BP5 Supporting: at least two cases with an alternate molecular basis; the other gene/disorder must be highly penetrant and the patient's personal/family history must demonstrate no overlap between the other disorder and PTEN.

Evidence considered

• The PTEN Expert Panel BP5 specification requires at least two cases, a highly penetrant alternate gene or disorder, and personal or family histories showing no overlap with PTEN.
• No qualifying alternate molecular diagnoses or case histories are available for this exact variant.

Still missing

• At least two cases with the exact variant and an alternate molecular basis are unavailable.
• Evidence for high penetrance of the alternate disorder and no phenotype overlap with PTEN is unavailable.

Sources