Variant classification summary

NM_000314.8:c.-666G>A

PTEN · NP_000305.3:p.? · NM_000314.8

GRCh37: chr10:89623561 G>A · GRCh38: chr10:87863804 G>A

Gene: PTEN Transcript: NM_000314.8

Final call

Benign

BA1 stand-alone benign

Variant details

Gene

PTEN

Transcript

NM_000314.8

Protein

NP_000305.3:p.?

gnomAD AF

0.000281764413930019 (v4.1)

ClinVar

Conflicting classifications of pathogenicity

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000314.8:c.-666G>A exceeds the PTEN VCEP BA1 allele frequency threshold with a gnomAD filtering allele frequency of 0.1076% (v2.1) and 0.1864% (v4.1), both above the 0.056% stand-alone benign cutoff. One homozygote is observed in gnomAD v4.1, inconsistent with an autosomal dominant high-penetrance disorder.

2

This is an upstream 5' UTR variant (c.-666G>A) with no predicted splicing impact (SpliceAI max delta = 0.04). Multiple benign-frequency observations and a homozygote in population databases support a benign interpretation.

Final determination: Rule17 in the Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Benign.

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	N/A	NM_000314.8:c.-666G>A is an upstream 5' UTR variant, not a null variant (nonsense, frameshift, or canonical splice site). The PTEN PVS1 decision tree does not apply to non-null variants.	pvs1_variant_assessment vcep_pvs1_decisiontree_pten
PS1	N/A	NM_000314.8:c.-666G>A is an upstream non-coding variant that does not alter the amino acid sequence. PS1 requires the same amino acid change as a known pathogenic variant.
PS2	Not met	No de novo observation data available for NM_000314.8:c.-666G>A. Neither proven nor assumed de novo events have been reported.
PS3	Not met	No functional data available for NM_000314.8:c.-666G>A. The PTEN VCEP PS3 functional assay (Mighell et al. 2018, mmc2.xlsx) covers missense variants only via phosphatase activity assay; this upstream variant is not represented. No splicing assay data available.	vcep_mmc2
PS4	Not met	No proband specificity score data available for NM_000314.8:c.-666G>A. The PTEN VCEP PS4 requires enumeration of probands with phenotype specificity scoring; no such data were identified.
PS5	N/A	PS5 is not a recognized ACMG/AMP criterion code. No assessment applicable.
PM1	N/A	NM_000314.8:c.-666G>A is an upstream non-coding variant and does not reside in any of the PTEN catalytic motif residues (NP_000305.3: 90-94, 123-130, 166-168) as defined by the PTEN VCEP PM1 specification.	cspec
PM2	Not met	NM_000314.8:c.-666G>A is present in gnomAD at frequencies well above the PTEN VCEP PM2_Supporting threshold of <0.001% (0.00001). gnomAD v2.1 overall AF = 0.0487% (15/30,802 alleles); gnomAD v4.1 overall AF = 0.0282% (109/386,848 alleles). The African/African American subpopulation AF is 0.1747% in v2.1 and 0.2205% in v4.1, far exceeding the subpopulation threshold of 0.002%.	gnomad_v2 gnomad_v4
PM5	N/A	NM_000314.8:c.-666G>A is an upstream non-coding variant, not a missense change. PM5 requires a missense change at an amino acid residue where a different pathogenic missense has been observed.	pm5_candidates
PM6	Not met	No de novo observation data available for NM_000314.8:c.-666G>A. No assumed or confirmed de novo events have been reported.
PP1	Not met	No co-segregation data available for NM_000314.8:c.-666G>A. No family studies with meiotic counts have been reported.
PP2	N/A	NM_000314.8:c.-666G>A is an upstream non-coding variant, not a missense variant. PP2 applies to missense variants in genes with a low rate of benign missense variation.	cspec
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. SpliceAI max delta score = 0.04, indicating no predicted splicing impact. REVEL and BayesDel scores are not available (non-coding variant). The PTEN VCEP PP3 threshold (REVEL >0.7 for missense; SpliceAI + VarSeak concordance for splicing) is not met.	spliceai cspec
PP4	N/A	PTEN VCEP specifies PP4 as Not Applicable. Phenotype specificity has been incorporated into PS4 rule specifications.	cspec
PP5	N/A	PTEN VCEP specifies PP5 as Not Applicable.	cspec
BA1	Met	NM_000314.8:c.-666G>A exceeds the PTEN VCEP BA1 allele frequency threshold. The gnomAD filtering allele frequency (grpmax FAF) is 0.001076 (0.1076%) in v2.1 and 0.001864 (0.1864%) in v4.1, both well above the 0.00056 (0.056%) stand-alone benign threshold. Additionally, one homozygote is observed in gnomAD v4.1 (African/African American population, genome data), which is inconsistent with an autosomal dominant highly penetrant disorder.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	The gnomAD filtering allele frequency for NM_000314.8:c.-666G>A (0.1076% v2.1, 0.1864% v4.1) exceeds the PTEN VCEP BS1 upper bound of 0.056%. The variant is captured by BA1 at the stand-alone benign level; BS1 is superseded.	gnomad_v2 gnomad_v4 cspec
BS2	Not met	One homozygote is observed in gnomAD v4.1 (genome data, African/African American population), but the clinical phenotype of this individual is unknown. The PTEN VCEP BS2 requires observation in a healthy or PHTS-unaffected individual; gnomAD population data alone do not confirm unaffected status. Additionally, BS2 would be downgraded to supporting if BS1 were also applied.	gnomad_v4
BS3	Not met	No functional studies demonstrating no damaging effect are available for NM_000314.8:c.-666G>A. The PTEN VCEP BS3_Strong requires an RNA/mini-gene splicing assay demonstrating no impact. The VCEP BS3_Supporting (phosphatase activity >0 per Mighell et al. 2018) applies only to missense variants. SpliceAI max delta of 0.04 is consistent with no splicing impact but does not substitute for a direct functional assay.	spliceai vcep_mmc2 cspec
BS4	Not met	No segregation data available for NM_000314.8:c.-666G>A. The PTEN VCEP BS4 requires lack of segregation in affected family members; no family studies have been reported.
BP1	N/A	PTEN VCEP specifies BP1 as Not Applicable.	cspec
BP2	Not met	No data available regarding NM_000314.8:c.-666G>A observed in trans with a pathogenic PTEN variant or in cis with multiple pathogenic PTEN variants.
BP3	N/A	Skipped per instructions.
BP4	Not met	NM_000314.8:c.-666G>A is an upstream 5' UTR variant. The PTEN VCEP BP4 specification applies to synonymous or intronic variants with concordant SpliceAI (0-0.2) and VarSeak (Class 1-2) benign predictions. While SpliceAI max delta is 0.04 (no predicted splice impact), the variant is not synonymous or intronic per the VCEP scope, and VarSeak data are not available.	spliceai cspec
BP5	Not met	No data available indicating NM_000314.8:c.-666G>A was found in a case with an alternate molecular basis for disease. The PTEN VCEP BP5 requires a variant found in a case with an alternate highly penetrant molecular diagnosis where phenotypes do not overlap.
BP6	N/A	PTEN VCEP specifies BP6 as Not Applicable.	cspec
BP7	N/A	NM_000314.8:c.-666G>A is an upstream 5' UTR variant (c.-666). The PTEN VCEP BP7 applies to synonymous or intronic variants at or beyond +7/-21 splice positions. This upstream variant is outside the BP7 scope.	cspec

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