PTENc.802-3T>AUncertain significance

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Variant interpretation report

PTEN c.802-3T>A, p.?

NM_000314.8:c.802-3T>A NP_000305.3:p.? View identifiers

Classification

Uncertain significance

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About PTEN

No gene-level summary was recorded for this case.

Key facts

Condition: PTEN hamartoma tumor syndrome
Inheritance: Autosomal dominant
Evidence used: 1 supporting (benign) · 1 supporting (pathogenic)
Expert rules: ClinGen PTEN VCEP v3.2
Other laboratories (ClinVar): 4 Uncertain significance · 2 Likely benign · 1 Uncertain Significance
Pipeline record: 25 Jul 2026 · version 7.0.4

Evidence considered

View criteria

Applied evidence criteria

PM2 (supporting): The variant is present at extremely low frequency in population databases, meeting the PTEN VCEP PM2_Supporting threshold. In gnomAD v4.1, it is observed in 1 of 1,585,530 alleles (AF=6.3×10⁻⁷; 0.000063%), which is well below the VCEP threshold of <0.001% (0.00001). The highest subpopulation frequency is in European (non-Finnish) at 1/1,168,048 alleles (AF=8.6×10⁻⁷; 0.000086%), also below the 0.002% subpopulation threshold. Absent from gnomAD v2.1 and gnomAD-Canada.
BP6 (supporting): Expert panel Clingen PTEN Variant Curation Expert Panel, Clingen classified as Likely benign.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.

01The reasoning

How it was classified

The recorded framework is ClinGen PTEN VCEP v3.2. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 1 Benign evidence criteria: 1

Pathogenic criteria applied · 1

PM2Supporting

PM2 · supporting

The variant is present at extremely low frequency in population databases, meeting the PTEN VCEP PM2_Supporting threshold. In gnomAD v4.1, it is observed in 1 of 1,585,530 alleles (AF=6.3×10⁻⁷; 0.000063%), which is well below the VCEP threshold of <0.001% (0.00001). The highest subpopulation frequency is in European (non-Finnish) at 1/1,168,048 alleles (AF=8.6×10⁻⁷; 0.000086%), also below the 0.002% subpopulation threshold. Absent from gnomAD v2.1 and gnomAD-Canada.

Benign criteria applied · 1

BP6Supporting

BP6 · supporting

Expert panel Clingen PTEN Variant Curation Expert Panel, Clingen classified as Likely benign.

Recorded classification: Uncertain significance

ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 v3.2 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, BP6 supporting benign; no rule matched the adjudicated criteria.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1

gnomAD v2.1

Population frequency

1 / 1,585,530 alleles

gnomAD v4.1: 1 / 1,585,530 alleles. Recorded AF 6.30704e-07. Recorded homozygote count 0.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

Applied · PM2 →

gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗

SpliceAI score

0.070 maximum delta

Recorded SpliceAI maximum delta score: 0.070. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗

ClinVar submissions

7 reported laboratory submissions

4 Uncertain significance · 2 Likely benign · 1 Uncertain Significance. ClinVar API review status: reviewed by expert panel.

Applied · BP6 → ClinVar ↗

No screenshot for this evidence

Functional evidence

Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

No listed criterion applied OncoKB ↗

Somatic evidence

No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Context only COSMIC ↗

For specialists

Technical detail

ACMG/AMP criteria under ClinGen PTEN VCEP v3.2, with the data and sources behind each one.

27 criteria with recorded statuses: 2 met · 16 not met · 0 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic

PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM5 PM6 PP1 PP2 PP3 PP4 PP5 PS5

Benign

BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7

Met Not met Not assessed Not applicable

NM_000314.8:c.802-3T>A is an intronic variant at position -3 of the acceptor splice site of PTEN intron 7. It is present at extremely low frequency in gnomAD v4.1 (1/1,585,530 alleles, AF=6.3×10⁻⁷).

This variant has been classified as Likely Benign by the ClinGen PTEN Variant Curation Expert Panel (ClinVar ID 135912, 3-star expert panel review).

SpliceAI predicts no significant splicing impact (max delta score = 0.07). Computational tools collectively predict no effect on normal splicing, as noted in one clinical laboratory submission.

The variant is absent from gnomAD v2.1 and observed only once in gnomAD v4.1, meeting PTEN VCEP PM2_Supporting due to extremely low population frequency.

BP6 is applied at supporting benign level based on the ClinGen PTEN EP classification of Likely Benign (3-star expert panel review).

No functional splicing assay, de novo, segregation, or case-control data is available for this variant. The overall evidence profile supports a likely benign interpretation consistent with the expert panel classification.

Met · 2

PM2 SupportingThe variant is present at extremely low frequency in population databases, meeting the PTEN VCEP PM2_Supporting threshold. In gnomAD v4.1, it is observed in 1 of 1,585,530 alleles (AF=6.3×10⁻⁷; 0.000063%), which is well below the VCEP threshold of <0.001% (0.00001). The highest subpopulation frequency is in European (non-Finnish) at 1/1,168,048 alleles (AF=8.6×10⁻⁷; 0.000086%), also below the 0.002% subpopulation threshold. Absent from gnomAD v2.1 and gnomAD-Canada. Details ▾Hide ▴

Evidence considered

gnomAD v4.1: AF=6.3×10⁻⁷ (1/1
585
530 alleles
0 homozygotes)
Best subpopulation NFE: AF=8.6×10⁻⁷
below 0.002% threshold
Absent from gnomAD v2.1 and gnomAD-Canada

Sources

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗cspec ↗

BP6 SupportingExpert panel Clingen PTEN Variant Curation Expert Panel, Clingen classified as Likely benign. Details ▾Hide ▴

Evidence considered

ClinVar variation ID 135912: Likely Benign
reviewed by expert panel (ClinGen PTEN VCEP
3-star)
ClinVar expert panel classification

Sources

clinvar ↗

Not met · 16 · evaluated, threshold not reached

PS2 No de novo occurrence data is available for this variant. The evidence packet contains no reports of confirmed or assumed de novo observations in patients with PTEN hamartoma tumor syndrome. Details ▾Hide ▴

Still missing

No de novo data available in ClinVar submissions or publications

PS3 No RNA, mini-gene, or other splicing assay data is available for this variant. The mmc2.xlsx (Mighell et al. 2018, PMID:29706350) phosphatase activity assay applies only to missense variants. One ClinVar submission (SCV001362395, LabCorp) explicitly states 'functional studies have not been reported for this variant.' The SCV004835524 submission also notes 'to our knowledge, functional studies have not been reported for this variant.' Details ▾Hide ▴

Evidence considered

No splicing assay (RNA/mini-gene) data available
Mighell 2018 phosphatase assay is missense-only
not applicable to splice site variants
ClinVar submissions confirm absence of reported functional studies

Still missing

No RNA/mini-gene splicing assay performed for this variant

Sources

clinvar ↗vcep_mmc2

PS4 No proband counting, case-control study, or PTEN specificity scoring data is available for this variant. The variant is present in ClinVar with submissions from several clinical laboratories, but no proband phenotype specificity scores have been calculated to meet the VCEP PS4 thresholds. Details ▾Hide ▴

Evidence considered

Variant observed in ClinVar submissions (8 total)
but no specificity scoring data

Still missing

No proband phenotype specificity scoring available

Sources

clinvar ↗

PM6 No assumed or confirmed de novo observations are reported for this variant in ClinVar or the literature. The PTEN VCEP PM6 rule requires at minimum an assumed de novo occurrence in a proband with disease and no family history. Details ▾Hide ▴

Still missing

No de novo data available

PP1 No co-segregation data is available for this variant. The PTEN VCEP PP1 rule requires at least 3-4 meioses for supporting-level evidence; no family studies or segregation analyses were identified in the evidence packet. Details ▾Hide ▴

Still missing

No segregation data available

PP3 The PTEN VCEP PP3 rule for splicing variants requires concordance of SpliceAI (score 0.5-1) and VarSeak (Class 4-5) predicting a splicing impact. SpliceAI max delta score for this variant is 0.07, far below the pathogenic range. No VarSeak data is available. The computational evidence does not support a deleterious effect on splicing; it supports the absence of impact. Details ▾Hide ▴

Evidence considered

SpliceAI max delta = 0.07 (well below 0.5 threshold for pathogenic prediction)
SpliceAI scores: DS_AG=0.07
DS_AL=0.0
DS_DG=0.0
DS_DL=0.01

Still missing

VarSeak score not available in evidence packet

Sources

spliceai ↗

PP5 The ClinVar expert panel classification for this variant is Likely Benign (ClinVar variation ID 135912), not Pathogenic or Likely Pathogenic. PP5 requires a reputable source reporting the variant as pathogenic. Although the PTEN VCEP marks PP5 as Not Applicable, even under the global ClinVar 3-star override rule, the EP classification of Likely Benign does not support PP5 (which requires a pathogenic assertion). Details ▾Hide ▴

Evidence considered

ClinVar EP classification is Likely Benign
not Pathogenic
PTEN VCEP marks PP5 as Not Applicable for this VCEP

Sources

clinvar ↗

BA1 The PTEN VCEP BA1 threshold requires gnomAD filtering allele frequency >0.056% (0.00056). The observed frequency in gnomAD v4.1 is 6.3×10⁻⁷ (0.000063%), far below the BA1 threshold. Details ▾Hide ▴

Evidence considered

gnomAD v4.1 AF=6.3×10⁻⁷
well below BA1 threshold of 0.00056

Sources

gnomad_v4 ↗cspec ↗

BS1 The PTEN VCEP BS1_Strong threshold requires AF 0.0043%-0.056% (0.000043-0.00056) and BS1_Supporting requires AF 0.00043%-0.0043% (0.0000043-0.000043). The observed gnomAD v4.1 AF of 6.3×10⁻⁷ (0.000063%) falls below even the supporting threshold. The variant is too rare to meet BS1 at any strength. Details ▾Hide ▴

Evidence considered

gnomAD v4.1 AF=6.3×10⁻⁷ (0.000063%)
below BS1_Supporting floor of 0.0000043 (0.00043%)

Sources

gnomad_v4 ↗cspec ↗

BS2 The PTEN VCEP BS2 rule requires observation in the homozygous state in a healthy or PHTS-unaffected individual. gnomAD v4.1 reports 0 homozygotes for this variant. No homozygous observations are recorded in any database. Details ▾Hide ▴

Evidence considered

gnomAD v4.1: homozygotes = 0 across all populations

Sources

gnomad_v4 ↗cspec ↗

BS3 The PTEN VCEP BS3 rule for intronic variants requires RNA, mini-gene, or other splicing assay demonstrating no splicing impact. No functional splicing assay data is available for this variant. The Mighell et al. 2018 (PMID:29706350) phosphatase assay in mmc2.xlsx applies only to missense variants. SpliceAI computational prediction alone does not qualify as a functional assay under BS3. Details ▾Hide ▴

Evidence considered

No RNA/mini-gene splicing assay data available
SpliceAI in silico prediction is not a functional assay

Still missing

No splicing assay performed for this variant

Sources

cspec ↗

BS4 No segregation data is available for this variant. The PTEN VCEP BS4 rule requires lack of segregation in affected family members; no family studies are present in the evidence packet. Details ▾Hide ▴

Still missing

No segregation data available

BP2 No evidence of this variant occurring in trans with a pathogenic/likely pathogenic PTEN variant or in cis with multiple different pathogenic/likely pathogenic PTEN variants. The PTEN VCEP BP2 rule requires such observations. Details ▾Hide ▴

Still missing

No trans/cis phase data available

BP4 The PTEN VCEP BP4 rule for intronic variants requires concordance of both SpliceAI (scores 0-0.2) and VarSeak (Class 1-2) predicting no splicing impact. SpliceAI max delta is 0.07, which falls in the benign range. However, VarSeak data is not available in the evidence packet, so the required concordance cannot be confirmed. One ClinVar submission (SCV001362395, LabCorp) notes '5/5 computational tools predict no significant impact on normal splicing,' consistent with a benign computational consensus, but without explicit VarSeak score the VCEP concordance requirement is not independently verifiable. Details ▾Hide ▴

Evidence considered

SpliceAI max delta = 0.07 (in benign range 0-0.2)
ClinVar SCV001362395: '5/5 computational tools predict no significant impact on normal splicing'

Still missing

VarSeak score not available
cannot confirm SpliceAI-VarSeak concordance required by VCEP

Sources

spliceai ↗cspec ↗clinvar ↗

BP5 The PTEN VCEP BP5 rule requires at least two cases where the variant is found in individuals with an alternate molecular basis for disease (highly penetrant other gene/disorder, with no phenotypic overlap with PTEN). No such cases are reported in the evidence packet. Details ▾Hide ▴

Still missing

No alternate molecular basis data available

PS5 PS5 requires a reputable source reporting the variant as pathogenic, with evidence not available for independent evaluation. The ClinVar expert panel (ClinGen PTEN VCEP) has classified this variant as Likely Benign, not Pathogenic. No reputable source reports this variant as pathogenic. Not met. Details ▾Hide ▴

Evidence considered

ClinVar EP classification is Likely Benign
not Pathogenic
No reputable source reports this variant as pathogenic

Sources

clinvar ↗

Not applicable · 9· recorded as not applicable Show reasons ▾Hide reasons ▴

PVS1 N/ANM_000314.8:c.802-3T>A is at position -3 of the intron 7 acceptor splice site, outside the canonical ±1,2 splice consensus positions. The PTEN VCEP PVS1 decision tree applies only to nonsense, frameshift, canonical GT-AG ±1,2 splice site disruptions, and exon deletions. Intronic variants at positions beyond ±2 are not eligible for PVS1. Details ▾Hide ▴

Evidence considered

Variant is at intron 7 position -3
not a canonical ±1
2 splice site
PTEN VCEP PVS1 decision tree applies only to canonical ±1
2 splice consensus disruptions and null variants

Sources

cspec ↗vcep_pvs1_decisiontree_pten

PS1 N/AVariant is intronic (c.802-3T>A) and does not result in an amino acid change. No known pathogenic splice variant exists at the same nucleotide position for comparison. The PTEN VCEP PS1 rule applies to same amino acid changes or same-nucleotide splice variants with equal or greater predicted impact; neither condition is met. Details ▾Hide ▴

Evidence considered

Intronic variant with no amino acid change
No known pathogenic variant at nucleotide position c.802-3

Sources

cspec ↗

PM1 N/AThis is an intronic variant at position c.802-3. The PTEN VCEP PM1 rule applies to amino acid residues within catalytic motifs (WPD loop residues 90-94, P-loop residues 123-130, TI-loop residues 166-168 of NP_000305.3). As an intronic variant, it does not alter any amino acid residue and cannot be assessed for hotspot or functional domain location. Details ▾Hide ▴

Evidence considered

Intronic variant
no amino acid residue affected

Sources

cspec ↗

PM5 N/APM5 applies to missense variants with a different pathogenic missense change at the same amino acid residue. NM_000314.8:c.802-3T>A is an intronic splice site variant, not a missense change. The pm5_candidates.json confirms the variant is not eligible for classic same-residue missense PM5: 'variant class is not missense-like.' Details ▾Hide ▴

Evidence considered

Variant is intronic
not missense
no amino acid residue affected

Sources

pm5_candidates

PP2 N/APP2 applies specifically to missense variants in genes with low rates of benign missense variation. NM_000314.8:c.802-3T>A is an intronic splice site variant, not a missense change. Details ▾Hide ▴

Evidence considered

Intronic variant
PP2 applies only to missense variants

Sources

cspec ↗

PP4 VCEPThe PTEN VCEP specifies PP4 as Not applicable. Phenotype specificity was incorporated into the PS4 rule specifications by the expert panel. Details ▾Hide ▴

Evidence considered

PTEN VCEP explicitly marks PP4 as Not applicable

Sources

cspec ↗

BP1 VCEPThe PTEN VCEP marks BP1 as Not applicable. This rule (missense variant in a gene where primarily truncating variants cause disease) is not applicable to PTEN per the expert panel specification. Details ▾Hide ▴

Evidence considered

PTEN VCEP explicitly marks BP1 as Not applicable

Sources

cspec ↗

BP3 VCEPBP3 applies to in-frame deletions/insertions in repetitive regions; this is a single nucleotide substitution in an intron. Details ▾Hide ▴

No further detail was recorded.

BP7 N/AThe PTEN VCEP BP7 rule for intronic variants requires the variant to be positioned at or beyond +7/-21 from the exon boundary. NM_000314.8:c.802-3T>A is at position -3 of intron 7 relative to exon 8, which is within the -1 to -21 zone (closer to the exon than position -21). This does not satisfy the VCEP positional requirement for BP7. Details ▾Hide ▴

Evidence considered

Variant at c.802-3 (position -3)
not at or beyond -21 as required by VCEP BP7

Sources

cspec ↗

Identifiers

Gene: PTEN
Transcript: NM_000314.8
Coding (HGVS c.): NM_000314.8:c.802-3T>A
Protein (HGVS p.): NP_000305.3:p.?
GRCh38: chr10:87960891 T>A
GRCh37: chr10:89720648 T>A
ClinVar: 135912

Gene diagram

Every interpreted variant in PTEN, mapped onto the exon structure of NM_000314.8. Select a row to find it on the plot.

PTENNM_000314.8

Fetching transcript structure from UCSC…

Exons

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Transcript span

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Strand

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Variants mapped

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Source

UCSC ncbiRefSeqCurated

All variants in PTEN — Select a row to find it on the plot; use the link to open its page.

	Protein	Location	Classification	Link

gnomAD v4.1 1 / 1,585,530 alleles AF 6.31e-07 · 0 homozygotes

gnomAD v2.1 Allele count data not recorded

gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 6.3e-07 · 1 / 1,585,530 alleles · 0 hom

European (non-Finnish)1 / 1,168,048

8.6e-07

0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 6.30704e-07; MAF= 0.00006%, 1/1585530 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.56129e-07; MAF= 0.00009%, 1/1168048 alleles, homozygotes = 0).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat +3 bp

0.000

SpliceAI acceptor gainat +46 bp

0.070

SpliceAI donor lossat +23 bp

0.010

SpliceAI donor gainat +46 bp

0.000

Pangolin splice lossmagnitude shown

-0.030

Pangolin splice gain

0.040

Other predictors

REVEL: Not available
BayesDel: Not available

How the predictions were used

Evidence considered

SpliceAI max delta = 0.07 (well below 0.5 threshold for pathogenic prediction)
SpliceAI scores: DS_AG=0.07
DS_AL=0.0
DS_DG=0.0
DS_DL=0.01

Still missing

VarSeak score not available in evidence packet

Sources

spliceai ↗

Evidence considered

SpliceAI max delta = 0.07 (in benign range 0-0.2)
ClinVar SCV001362395: '5/5 computational tools predict no significant impact on normal splicing'

Still missing

VarSeak score not available
cannot confirm SpliceAI-VarSeak concordance required by VCEP

Sources

spliceai ↗cspec ↗clinvar ↗

Evidence considered

Variant at c.802-3 (position -3)
not at or beyond -21 as required by VCEP BP7

Sources

cspec ↗

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).

8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E et al. · 2007

Discusses aberrant 5' splice site mutation patterns and computational prediction tools in human disease genes. NM_000314.8:c.802-3T>A was not identified in this paper.
Does not name this variant
PMID 17576681 ↗
ACMG policy statement: updated recommendations regarding analysis and reporting

ACMG policy statement on updated recommendations regarding analysis and reporting of secondary findings. NM_000314.8:c.802-3T>A was not identified.
Does not name this variant
PMID 25356965 ↗
Standards and guidelines for the interpretation of sequence variants: a joint co

ACMG/AMP standards and guidelines for the interpretation of sequence variants (Richards et al. 2015). This is a general framework paper; NM_000314.8:c.802-3T>A was not identified.
Does not name this variant
PMID 25741868 ↗
Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version.

PDQ cancer genetics information summary on breast and gynecologic cancers. NM_000314.8:c.802-3T>A was not identified.
Does not name this variant
PMID 26389210 ↗
Recommendations for reporting of secondary findings in clinical exome and genome

ACMG SF v2.0 recommendations for reporting secondary findings in clinical exome and genome sequencing (Kalia et al. 2016). PTEN is listed in the secondary findings gene table. NM_000314.8:c.802-3T>A was not identified.
Does not name this variant
PMID 27854360 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification crite

Sherloc refinement of the ACMG/AMP variant classification criteria (Nykamp et al. 2017). NM_000314.8:c.802-3T>A was not identified in this paper.
Does not name this variant
PMID 28492532 ↗
ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG).

Miller DT et al. · 2021

ACMG SF v3.0 recommendations for reporting secondary findings in clinical exome and genome sequencing (Miller et al. 2021). PTEN is listed in the secondary findings gene table. NM_000314.8:c.802-3T>A was not identified.
Does not name this variant
PMID 34012068 ↗
ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG).

Miller DT et al. · 2022

ACMG SF v3.1 list for reporting secondary findings in clinical exome and genome sequencing. NM_000314.8:c.802-3T>A was not identified.
Does not name this variant
PMID 35802134 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 1 / 1,585,530 recorded alleles Open source ↗

gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗

SpliceAI Lookup Recorded maximum delta 0.070 Open source ↗

ClinVar 4 Uncertain significance · 2 Likely benign · 1 Uncertain Significance Open source ↗

COSMIC Captured COSMIC source record Open source ↗

ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Uncertain significance (4 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely Benign by Clingen PTEN Variant Curation Expert Panel, Clingen (expert panel). (ClinVarID = 135912)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).

Somatic

This variant has not previously been reported in somatic cancers (COSMIC).