Variant classification summary

NM_000314.8:c.165-7T>C

PTEN · NP_000305.3:p.? · NM_000314.8

GRCh37: chr10:89685263 T>C · GRCh38: chr10:87925506 T>C

Gene: PTEN Transcript: NM_000314.8

Final call

VUS

BS1 strong benign

Variant details

Gene

PTEN

Transcript

NM_000314.8

Protein

NP_000305.3:p.?

gnomAD AF

6.9308540198323235e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000314.8:c.165-7T>C is an intronic variant in PTEN located at position -7 of the intron 2 splice acceptor region.

2

This variant is present in gnomAD v4.1 at a grpmax filtering allele frequency of 0.006% (11/1,587,106 alleles), which falls within the PTEN VCEP BS1_Strong range (0.0043%-0.056%), indicating the variant is observed at a population frequency greater than expected for a highly penetrant autosomal dominant disorder.

3

The variant is classified as Likely benign in ClinVar (VCV000412808) by 5 clinical laboratories, consistent with the population frequency evidence.

4

SpliceAI predicts no significant splicing impact (max delta score = 0.02), which falls within the benign range for computational splice prediction but is not sufficient alone to apply BP4 under the PTEN VCEP without VarSeak concordance.

5

No pathogenic computational predictions, functional assay data, segregation evidence, de novo observations, or case-level phenotype data were identified to support pathogenicity for this variant.

6

The variant does not meet PM2 under PTEN VCEP rules because the South Asian subpopulation frequency (0.0111%) exceeds the VCEP subpopulation threshold of 0.002%.

Final determination: No criteria-combination rule matched the adjudicated criteria in the Richards et.al., 2015 - Combining rules v3.2.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	The variant NM_000314.8:c.165-7T>C is an intronic substitution at position -7, which is not a canonical GT-AG ±1 or ±2 splice site. The PTEN VCEP PVS1 decision tree (v3.2.0) applies only to nonsense, frameshift, canonical splice site disruptions, and CNV deletions. An intronic variant at position -7 falls outside the scope of the PVS1 decision tree.	vcep_pvs1_decisiontree_pten cspec pvs1_variant_assessment
PS1	Not met	No previously established pathogenic variant has been identified at the same nucleotide position (c.165-7) in PTEN. The ClinVar record for this variant (VCV000412808) carries a Likely benign classification from 5 clinical laboratories, and no pathogenic comparator at this position was found.	clinvar cspec
PS2	Not met	No de novo observations (confirmed or assumed) were identified for NM_000314.8:c.165-7T>C in the available evidence. No publications report a de novo occurrence of this variant in a patient with PTEN hamartoma tumor syndrome and no family history.
PS3	Not met	No RNA, mini-gene, or other splicing assay data are available for this intronic variant. The Mighell et al. 2018 (PMID: 29706350) phosphatase activity assay applies to missense variants only; this variant is intronic and has no protein-level consequence. SpliceAI predicts no significant splicing impact (max delta = 0.02).	spliceai cspec vcep_mmc2
PS4	Not met	No proband counts or case-control data with PTEN phenotype specificity scores are available for this variant. The ClinVar record lists 5 clinical laboratory submissions classifying it as Likely benign, but no proband-level phenotype data suitable for PTEN VCEP PS4 specificity scoring were identified.	clinvar
PS5	N/A	This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee (PTEN VCEP v3.2.0). PP5 (the benign counterpart) is also marked Not Applicable for this VCEP.	cspec
PM1	N/A	This is an intronic variant (c.165-7) that does not alter any amino acid residue. PTEN VCEP PM1 applies only to variants located in catalytic motifs at residues 90-94 (WPD loop), 123-130 (P-loop), or 166-168 (TI-loop) of NP_000305.3.	cspec
PM2	Not met	Under PTEN VCEP v3.2.0, PM2_Supporting requires total gnomAD allele frequency <0.001% (0.00001) AND subpopulation AF <0.002% (0.00002) when multiple alleles are present. Although the total gnomAD v4.1 AF is 0.00069% (<0.001%), the South Asian subpopulation has AF = 0.0111% (10/90,108 alleles), which exceeds the 0.002% subpopulation threshold. The variant therefore fails PM2 under VCEP rules.	gnomad_v4 cspec
PM5	N/A	This is an intronic substitution, not a missense variant. PTEN VCEP PM5 applies only to missense changes at an amino acid residue where a different pathogenic or likely pathogenic missense change has been previously established.	cspec pm5_candidates
PM6	Not met	No assumed or confirmed de novo observations were identified for this variant in the available evidence. No publications report a de novo occurrence in a proband with PTEN hamartoma tumor syndrome.
PP1	Not met	No co-segregation data are available for this variant. No publications report segregation analysis in families with this variant and PTEN-associated phenotypes.
PP2	N/A	This is an intronic variant, not a missense variant. PTEN VCEP PP2 applies specifically to missense variants in a gene with a low rate of benign missense variation where missense variants are a common disease mechanism.	cspec
PP3	Not met	Under PTEN VCEP v3.2.0, PP3 for splicing variants requires concordance of SpliceAI (scores 0.5-1, pathogenic range) and VarSeak (Class 4-5). The SpliceAI max delta score for this variant is 0.02, which is far below the 0.5 pathogenic threshold and indicates no predicted splicing impact. PP3 is not supported.	spliceai cspec
PP4	N/A	PTEN VCEP v3.2.0: Phenotype specificity has been incorporated into the PS4 rule specifications. PP4 is not applicable under this VCEP.	cspec
PP5	N/A	This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee (PTEN VCEP v3.2.0).	cspec
BA1	Not met	PTEN VCEP v3.2.0 BA1 requires gnomAD filtering allele frequency >0.056% (0.00056). The gnomAD v4.1 grpmax filtering allele frequency is 5.997e-05 (0.006%), which is approximately 10-fold below the BA1 threshold.	gnomad_v4 cspec
BS1	Met	PTEN VCEP v3.2.0 BS1_Strong applies when gnomAD filtering allele frequency is between 0.0043% (0.000043) and 0.056% (0.00056). The gnomAD v4.1 grpmax filtering allele frequency for this variant is 5.997e-05 (0.006%), which falls within the BS1_Strong range. This indicates the variant is observed at a population frequency greater than expected for a highly penetrant autosomal dominant disorder like PTEN hamartoma tumor syndrome.	gnomad_v4 cspec
BS2	Not met	PTEN VCEP v3.2.0 BS2 requires observation in the homozygous state in a healthy or PHTS-unaffected individual. No homozygous observations are present in gnomAD v2.1 or v4.1 (homozygotes = 0 in both datasets).	gnomad_v2 gnomad_v4 cspec
BS3	Not met	No RNA, mini-gene, or other splicing assay data demonstrating no splicing impact are available for this intronic variant. PTEN VCEP BS3_Strong requires a splicing assay showing no impact. The Mighell et al. 2018 phosphatase activity assay (BS3_Supporting) applies to missense variants only. SpliceAI delta of 0.02 alone is insufficient to satisfy the VCEP BS3 functional evidence requirement.	spliceai cspec vcep_mmc2
BS4	Not met	No segregation data demonstrating lack of segregation in affected family members are available for this variant. PTEN VCEP BS4 requires two or more families for strong evidence, or one family for supporting evidence.
BP1	N/A	PTEN VCEP v3.2.0: This rule is not applicable to PTEN. BP1 (missense variant in a gene where primarily truncating variants cause disease) does not apply because both missense and truncating variants are established disease mechanisms in PTEN.	cspec
BP2	Not met	No observations of this variant in trans with a pathogenic or likely pathogenic PTEN variant, nor three or more observations in cis/phase-unknown with different P/LP PTEN variants, were identified in the available evidence.
BP4	Not assessed	PTEN VCEP v3.2.0 BP4 requires concordance of BOTH SpliceAI (scores 0-0.2 considered benign) AND VarSeak (Class 1-2 considered benign) predicting no splicing impact. The SpliceAI max delta score is 0.02, which falls within the benign range and would support BP4. However, VarSeak data are not available for this variant, precluding full VCEP-concordant assessment. BP4 cannot be applied without VarSeak data to confirm concordance.	spliceai cspec
BP5	Not met	PTEN VCEP v3.2.0 BP5 requires at least two cases where the variant is found in individuals with an alternate molecular basis for disease, where the other gene/disorder is highly penetrant and there is no phenotypic overlap with PTEN. No such cases were identified in the available evidence.
BP6	N/A	This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee (PTEN VCEP v3.2.0). ClinVar classification as Likely benign from 5 laboratories is noted but does not constitute an applicable BP6 criterion under this VCEP.	cspec clinvar
BP7	N/A	PTEN VCEP v3.2.0 BP7 requires an intronic variant to be positioned at or beyond +7 (donor site) or -21 (acceptor site) relative to the exon boundary. This variant at c.165-7 is located at position -7 in the intron 2 acceptor region, which is within the splice-region (not deep intronic) and does not meet the positional threshold for BP7 applicability.	cspec
BP3	N/A	Intronic substitution variant; BP3 applies to in-frame deletions/insertions in repetitive regions, which is not relevant to this variant type.
PM3	N/A	Autosomal dominant disorder criterion; PM3 (detected in trans with a pathogenic variant) applies to recessive disorders and is not applicable to PTEN hamartoma tumor syndrome.	cspec
PM4	N/A	Intronic substitution variant; PM4 applies to protein length changes due to in-frame deletions/insertions or stop-loss variants, none of which are relevant to this intronic substitution.

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