0%
PTENc.492+14dupLikely benign
Print report
Variant interpretation report

PTEN c.492+14dup, p.?

NM_000314.8:c.492+14dup NP_000305.3:p.? View identifiers
Classification
Likely benign

Variant description:

No variant summary was recorded for this case.

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

Likely benign.A likely benign classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About PTEN

No gene-level summary was recorded for this case.

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 v3.2.0. 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: 0 Benign evidence criteria: 2
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 2
BS1Strong
BS1 · strong

BS1_Strong under PTEN VCEP applies when gnomAD filtering allele frequency is 0.0043% to 0.056%. The gnomAD v4.1 grpmax filtering AF for c.492+14dup is 5.81e-05 (0.0058%), which falls within the BS1_Strong range (0.0043%-0.056%). This variant is observed at a population frequency higher than expected for a fully penetrant PTEN pathogenic variant causing PHTS.

BP7Supporting
BP7 · supporting

BP7 under PTEN VCEP applies to intronic variants at or beyond +7/-21 for which splicing prediction algorithms predict no impact. c.492+14dup is located at position +14 in intron 5 (beyond the +7 threshold). SpliceAI predicts no significant splice impact (max delta score 0.03), and the variant does not create a new splice site.

Recorded classification: Likely benign

Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule20 (1 Benign.Strong) with applied criteria: BS1 strong benign, BP7 supporting benign; maps to Likely Benign.

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
4 / 1,601,512 alleles

gnomAD v4.1: 4 / 1,601,512 alleles. Recorded AF 2.49764e-06. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.98969e-06; MAF= 0.00040%, 1/250646 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.8241e-06; MAF= 0.00088%, 1/113326 alleles, homozygotes = 0).

Applied · BS1 →
gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗
SpliceAI score
0.030 maximum delta

Recorded SpliceAI maximum delta score: 0.030. Refer to the recorded PP3/BP4 rationale for interpretation.

Applied · BP7 → SpliceAI ↗
ClinVar submissions
4 reported laboratory submissions

3 Likely benign · 1 Benign.

Context only 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 v3.2.0, with the data and sources behind each one.

28 criteria with recorded statuses: 2 met · 6 not met · 9 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM4PM5PM6PP1PP2PP3PP4PP5PS5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

BS1_Strong is met: the gnomAD v4.1 grpmax filtering allele frequency is 5.81e-05 (0.0058%), which falls within the PTEN VCEP BS1_Strong range of 0.0043%-0.056%. This population frequency is higher than expected for a fully penetrant pathogenic PTEN variant causing PHTS.

BP7_Supporting is met: c.492+14dup is an intronic variant at position +14 (beyond +7). SpliceAI predicts no significant splice impact (max delta score 0.03) and no creation of a cryptic splice site, meeting the PTEN VCEP BP7 criteria.

PM2_Supporting is not met: although the overall gnomAD allele frequency is very low (v4.1: 0.00025%), the Middle Eastern subpopulation in gnomAD v4.1 has 2 alleles out of 6,068 (AF 0.033%), which exceeds the PTEN VCEP subpopulation threshold of 0.002% for multiple alleles.

PVS1 is not met: this intronic duplication at c.492+14 does not qualify as a null variant under the PTEN PVS1 decision tree, and SpliceAI predicts no splice disruption.

Combined classification: 1 strong benign criterion (BS1) + 1 supporting benign criterion (BP7) yields a classification of Likely Benign per the ACMG/AMP combining rules adopted by the PTEN VCEP.

Met · 2

BS1 StrongBS1_Strong under PTEN VCEP applies when gnomAD filtering allele frequency is 0.0043% to 0.056%. The gnomAD v4.1 grpmax filtering AF for c.492+14dup is 5.81e-05 (0.0058%), which falls within the BS1_Strong range (0.0043%-0.056%). This variant is observed at a population frequency higher than expected for a fully penetrant PTEN pathogenic variant causing PHTS. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF = 5.81e-05 (0.0058%)
  • within PTEN VCEP BS1_Strong range of 0.0043%-0.056%.
Sources
gnomad_v4 ↗cspec ↗
BP7 SupportingBP7 under PTEN VCEP applies to intronic variants at or beyond +7/-21 for which splicing prediction algorithms predict no impact. c.492+14dup is located at position +14 in intron 5 (beyond the +7 threshold). SpliceAI predicts no significant splice impact (max delta score 0.03), and the variant does not create a new splice site. Details ▾Hide ▴
Evidence considered
  • Intronic position +14 (beyond +7 threshold).
  • SpliceAI max delta 0.03 — predicts no splice impact.
  • No cryptic splice site creation predicted.
Sources
spliceai ↗cspec ↗

Not met · 6 · evaluated, threshold not reached

PVS1 PVS1 is not applicable to this intronic variant (c.492+14dup). The PTEN PVS1 decision tree (VCEP v3.2.0) only covers nonsense, frameshift, canonical ±1,2 splice site disruptions, initiation codon variants, and single/multi-exon deletions. This variant is a deep intronic duplication that does not fall into any PVS1-qualifying variant class. SpliceAI predicts no significant splice impact (max delta 0.03). Details ▾Hide ▴
Evidence considered
  • Intronic duplication at c.492+14 (intron 5) is not a null variant class eligible for PVS1 under the PTEN VCEP decision tree.
  • SpliceAI max delta score 0.03 — no predicted splice disruption.
Sources
spliceai ↗cspec ↗
PM2 The overall gnomAD frequency is very low (v4.1: 4/1,601,512, AF = 0.00025%), meeting the PTEN VCEP main threshold of <0.001%. However, the PTEN VCEP PM2 rule also requires that if multiple alleles are present in any subpopulation, the subpopulation AF must be <0.002% (0.00002). In gnomAD v4.1, the Middle Eastern subpopulation has 2 alleles out of 6,068 (AF = 0.033%), exceeding the 0.002% subpopulation threshold. Therefore PM2_Supporting is not met. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1: 4/1
  • 601
  • 512 total alleles (AF 0.00025%).
  • Middle Eastern subpopulation: 2/6
  • 068 alleles (AF 0.033%)
  • exceeding PTEN VCEP subpopulation threshold of 0.002% for multiple alleles.
Sources
gnomad_v4 ↗
PP3 PP3 under PTEN VCEP requires SpliceAI scores of 0.5-1.0 for splicing variants (with VarSeak concordance). SpliceAI max delta score for c.492+14dup is 0.03, which is far below the 0.5 threshold. REVEL and BayesDel are not applicable (not SNV). No computational evidence supports a deleterious effect. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta score 0.03 — well below PP3 threshold of 0.5.
  • REVEL and BayesDel not applicable (not SNV).
Sources
spliceai ↗
BA1 BA1 under PTEN VCEP requires gnomAD filtering allele frequency >0.056% (0.00056). The v4.1 grpmax filtering AF is 0.0058% (5.81e-05), which is an order of magnitude below the BA1 threshold. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF = 5.81e-05 (0.0058%)
  • below BA1 threshold of 0.056%.
Sources
gnomad_v4 ↗
BS2 BS2 under PTEN VCEP requires observation of the variant in the homozygous state in a healthy or PHTS-unaffected individual. This variant has zero homozygotes in gnomAD v2.1 (0/250,646) and v4.1 (0/1,601,512). No homozygous observations are documented. Details ▾Hide ▴
Evidence considered
  • 0 homozygotes in gnomAD v2.1 and v4.1.
Sources
gnomad_v2 ↗gnomad_v4 ↗
BP4 BP4 under PTEN VCEP requires concordance of SpliceAI and VarSeak predicting no splicing impact (SpliceAI 0-0.2, VarSeak Class 1-2). SpliceAI max delta score for c.492+14dup is 0.03, which falls within the 0-0.2 range. However, VarSeak data are not available, and the PTEN VCEP requires concordance of both tools. A single computational prediction is insufficient to meet BP4. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta 0.03 (within BP4 threshold of 0-0.2).
  • VarSeak data not available
  • PTEN VCEP requires concordance of both tools.
Still missing
  • VarSeak prediction not available.
Sources
spliceai ↗

Not assessed · 9 · no assessment recorded

PS2 No de novo observations of NM_000314.8:c.492+14dup have been identified in ClinVar, LOVD, or published literature. Without a confirmed de novo occurrence in a patient with PTEN hamartoma tumor syndrome and no family history, PS2 cannot be applied. Details ▾Hide ▴
Evidence considered
  • No de novo data available for this variant.
Still missing
  • No trio or de novo testing data available.
PS3 No RNA, mini-gene, or splicing functional assay data are available for c.492+14dup. The Mighell et al. 2018 (PMID:29706350) phosphatase activity assay (mmc2.xlsx) covers missense variants only and does not include this intronic variant. No functional evidence supports a damaging effect. Details ▾Hide ▴
Evidence considered
  • Not found in Mighell et al. 2018 PTEN saturation mutagenesis dataset (missense only).
  • No RNA/mini-gene splicing assay data available.
Still missing
  • No functional data for this intronic variant.
PS4 No proband counts, specificity scores, or case-control studies are available for this variant. The PTEN VCEP PS4 criteria require proband specificity scoring, which cannot be performed without individual-level phenotype data. ClinVar classifies this variant as Likely benign/Benign, suggesting no enrichment in affected individuals. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Likely benign (3 labs)
  • Benign (1 lab). No proband specificity data available.
Still missing
  • No proband-level phenotype data for specificity scoring.
Sources
clinvar ↗
PM6 No assumed de novo observations of c.492+14dup have been reported in ClinVar, LOVD, or published literature. PM6 requires an assumed de novo occurrence in a proband with disease and no family history. Details ▾Hide ▴
Evidence considered
  • No assumed de novo data available.
Still missing
  • No de novo assertions in any database.
PP1 No co-segregation data are available for c.492+14dup. The PTEN VCEP requires at least 3-4 meioses for PP1_Supporting; no family studies involving this variant have been published. Details ▾Hide ▴
Evidence considered
  • No co-segregation data available.
Still missing
  • No family or segregation studies.
BS3 BS3_Strong under PTEN VCEP for intronic variants requires RNA/mini-gene assay demonstrating no splicing impact. No such functional data are available for c.492+14dup. BS3_Supporting (phosphatase activity >0 per Mighell et al. 2018) applies only to missense variants. SpliceAI prediction of no impact (max delta 0.03) is computational, not functional evidence. Details ▾Hide ▴
Evidence considered
  • No RNA/mini-gene splicing assay data available.
  • SpliceAI max delta 0.03 is computational
  • not functional evidence.
Still missing
  • No functional splicing assay data.
Sources
spliceai ↗
BS4 No segregation data are available for c.492+14dup. BS4 under PTEN VCEP requires lack of segregation in affected family members; no such studies have been published for this variant. Details ▾Hide ▴
Evidence considered
  • No segregation data available.
Still missing
  • No family segregation studies.
BP2 No observations of c.492+14dup in trans with a pathogenic/likely pathogenic PTEN variant or in cis with multiple P/LP PTEN variants have been reported. Phased data are not available from population databases. Details ▾Hide ▴
Evidence considered
  • No cis or trans observations with known pathogenic PTEN variants.
Still missing
  • No phased genotype data available.
BP5 BP5 under PTEN VCEP requires at least two cases where the variant is found with an alternate molecular basis for disease, with no phenotypic overlap. No such cases have been reported for c.492+14dup. Details ▾Hide ▴
Evidence considered
  • No cases with alternate molecular basis reported.
Still missing
  • No alternate-diagnosis cases identified.
Not applicable · 11· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/APS1 applies to same amino acid change as known pathogenic variant or different nucleotide at same position as a known pathogenic splicing variant. This is an intronic duplication (c.492+14dup) with no known pathogenic variant at this intronic position. Details ▾Hide ▴
Evidence considered
  • Intronic variant
  • no known pathogenic comparator at c.492+14.
PM1 N/APM1 under PTEN VCEP applies only to variants located in catalytic motif residues (NP_000305.3: 90-94, 123-130, 166-168). c.492+14dup is an intronic variant that does not alter any amino acid residue and lies outside all catalytic domains. Details ▾Hide ▴
Evidence considered
  • Intronic variant
  • no impact on catalytic motif residues.
PM4 N/APM4 under PTEN VCEP applies to in-frame insertions/deletions impacting a catalytic motif residue or causing protein extension. c.492+14dup is an intronic duplication that does not alter protein length or affect any catalytic motif residue. Details ▾Hide ▴
Evidence considered
  • Intronic duplication
  • no protein length change.
PM5 N/APM5 under PTEN VCEP applies to missense changes at a residue where a different pathogenic/likely pathogenic missense change has been observed. This is an intronic duplication, not a missense variant. pm5_candidates.json confirms no eligible comparators. Details ▾Hide ▴
Evidence considered
  • Intronic variant
  • PM5 is missense-specific.
PP2 N/APP2 under PTEN VCEP applies to missense variants in a gene with a low rate of benign missense variation. This is an intronic duplication, not a missense variant. Details ▾Hide ▴
Evidence considered
  • Intronic variant
  • PP2 is missense-specific.
PP4 VCEPPP4 is deemed Not Applicable by the PTEN VCEP v3.2.0. Phenotype specificity has been incorporated into the PS4 rule specifications. Details ▾Hide ▴
Evidence considered
  • PTEN VCEP explicitly marks PP4 as Not Applicable.
Sources
cspec ↗
PP5 VCEPPP5 is deemed Not Applicable for this VCEP by the PTEN Expert Panel v3.2.0. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Details ▾Hide ▴
Evidence considered
  • PTEN VCEP explicitly marks PP5 as Not Applicable for this VCEP.
Sources
cspec ↗
BP1 VCEPBP1 is deemed Not Applicable by the PTEN VCEP v3.2.0. This rule (missense variant in gene where primarily truncating variants cause disease) is not applicable to PTEN. Details ▾Hide ▴
Evidence considered
  • PTEN VCEP explicitly marks BP1 as Not Applicable.
Sources
cspec ↗
BP3 VCEPBP3 is deemed Not Applicable by the PTEN VCEP v3.2.0. This rule (in-frame deletions/insertions in repetitive regions) is not applicable to PTEN. Details ▾Hide ▴
Evidence considered
  • PTEN VCEP explicitly marks BP3 as Not Applicable.
Sources
cspec ↗
BP6 VCEPBP6 is deemed Not Applicable for this VCEP by the PTEN Expert Panel v3.2.0. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Details ▾Hide ▴
Evidence considered
  • PTEN VCEP explicitly marks BP6 as Not Applicable for this VCEP.
Sources
cspec ↗
PS5 N/APS5 is not a defined criterion in the ACMG/AMP 2015 framework or the PTEN VCEP v3.2.0 specifications. No such criterion exists for variant classification. Details ▾Hide ▴
Evidence considered
  • PS5 is not an ACMG/AMP criterion.

Identifiers

Gene
PTEN
Transcript
NM_000314.8
Coding (HGVS c.)
NM_000314.8:c.492+14dup
Protein (HGVS p.)
NP_000305.3:p.?
GRCh38
chr10:87933259 A>AT
GRCh37
chr10:89693016 A>AT
ClinVar
419168

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…
gnomAD v4.1 4 / 1,601,512 alleles AF 2.5e-06 · 0 homozygotes · FAF 5.81e-05
gnomAD v2.1 1 / 250,646 alleles AF 3.99e-06 · 0 homozygotes
gnomAD-Canada v1.0 0 / 0 alleles AF 0 · 0 homozygotes · FAF 0

By genetic ancestry

gnomAD v4.1

AF 2.5e-06 · 4 / 1,601,512 alleles · 0 hom · FAF 5.8e-05
Middle Eastern2 / 6,068 0.00033
European (non-Finnish)2 / 1,168,784 1.7e-06
0 alternate alleles recorded in 8 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, South Asian, Ashkenazi Jewish, African/African American.

gnomAD v2.1

AF 4e-06 · 1 / 250,646 alleles · 0 hom
European (non-Finnish)1 / 113,326 8.8e-06
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.

gnomAD-Canada

AF 0 · 0 / 0 alleles · 0 hom

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 2.49764e-06; MAF= 0.00025%, 4/1601512 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000329598; MAF= 0.03296%, 2/6068 alleles, homozygotes = 0); grpmax FAF= 5.813e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.98969e-06; MAF= 0.00040%, 1/250646 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.8241e-06; MAF= 0.00088%, 1/113326 alleles, homozygotes = 0).

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

SpliceAI acceptor lossat -58 bp
0.000
SpliceAI acceptor gainat -264 bp
0.030
SpliceAI donor lossat +378 bp
0.000
SpliceAI donor gainat -8 bp
0.000
Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.000

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

BP7 SupportingBP7 under PTEN VCEP applies to intronic variants at or beyond +7/-21 for which splicing prediction algorithms predict no impact. c.492+14dup is located at position +14 in intron 5 (beyond the +7 threshold). SpliceAI predicts no significant splice impact (max delta score 0.03), and the variant does not create a new splice site. Details ▾Hide ▴
Evidence considered
  • Intronic position +14 (beyond +7 threshold).
  • SpliceAI max delta 0.03 — predicts no splice impact.
  • No cryptic splice site creation predicted.
Sources
spliceai ↗cspec ↗
PP3 PP3 under PTEN VCEP requires SpliceAI scores of 0.5-1.0 for splicing variants (with VarSeak concordance). SpliceAI max delta score for c.492+14dup is 0.03, which is far below the 0.5 threshold. REVEL and BayesDel are not applicable (not SNV). No computational evidence supports a deleterious effect. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta score 0.03 — well below PP3 threshold of 0.5.
  • REVEL and BayesDel not applicable (not SNV).
Sources
spliceai ↗
BP4 BP4 under PTEN VCEP requires concordance of SpliceAI and VarSeak predicting no splicing impact (SpliceAI 0-0.2, VarSeak Class 1-2). SpliceAI max delta score for c.492+14dup is 0.03, which falls within the 0-0.2 range. However, VarSeak data are not available, and the PTEN VCEP requires concordance of both tools. A single computational prediction is insufficient to meet BP4. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta 0.03 (within BP4 threshold of 0-0.2).
  • VarSeak data not available
  • PTEN VCEP requires concordance of both tools.
Still missing
  • VarSeak prediction not available.
Sources
spliceai ↗

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).

9 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

  • Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.
    No paper-specific finding is recorded.
    PMID 23918944 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    No paper-specific finding is recorded.
    PMID 25741868 ↗
  • American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility.
    American Society of Clinical Oncology · 2003
    No paper-specific finding is recorded.
    PMID 12692171 ↗
  • Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
    Trepanier A et al. · 2004
    No paper-specific finding is recorded.
    PMID 15604628 ↗
  • American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.
    Saslow D et al. · 2007
    No paper-specific finding is recorded.
    PMID 17392385 ↗
  • Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors.
    Berliner JL et al. · 2007
    No paper-specific finding is recorded.
    PMID 17508274 ↗
  • The emerging landscape of breast cancer susceptibility.
    Stratton MR et al. · 2008
    No paper-specific finding is recorded.
    PMID 18163131 ↗
  • ACOG Practice Bulletin No. 103: Hereditary breast and ovarian cancer syndrome.
    2009
    No paper-specific finding is recorded.
    PMID 19305347 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    No paper-specific finding is recorded.
    PMID 28492532 ↗

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

gnomAD v4.1 4 / 1,601,512 recorded alleles Open source ↗
gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗
SpliceAI Lookup Recorded maximum delta 0.030 Open source ↗
ClinVar 3 Likely benign · 1 Benign 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

This variant is present in gnomAD v4.1 (AF= 2.49764e-06; MAF= 0.00025%, 4/1601512 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000329598; MAF= 0.03296%, 2/6068 alleles, homozygotes = 0); grpmax FAF= 5.813e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.98969e-06; MAF= 0.00040%, 1/250646 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.8241e-06; MAF= 0.00088%, 1/113326 alleles, homozygotes = 0).

ClinVar

This variant has been reported in ClinVar as Likely benign (3 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 419168)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).

Somatic

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