Starting
Initialising…
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PALB2
Final classification
VUS
PALB2 c.82T>A · p.Tyr28Asn
PALB2

NM_024675.3:c.82T>A (p.Tyr28Asn) is a missense variant in PALB2. It is absent from gnomAD v2.1 and v4.1, meeting PM2_Supporting per PALB2 VCEP v1.2.0 (allele frequency ≤ 0.000333%).

Gene
PALB2
Transcript
NM_024675.3
HGVS · transcript:coding
NM_024675.3:c.82T>A
Consequence
N/A
GRCh38
chr16:23638096 A>T
GRCh37
chr16:23649417 A>T
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, BP1 supporting benign; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, BP1 supporting benign; no rule matched the adjudicated criteria.
Classification rationale
PM2 BP1 VUS
PALB2 c.82T>A

NM_024675.3:c.82T>A (p.Tyr28Asn) is a missense variant in PALB2. It is absent from gnomAD v2.1 and v4.1, meeting PM2_Supporting per PALB2 VCEP v1.2.0 (allele frequency ≤ 0.000333%).1 BP1_Supporting is applied as the PALB2 VCEP v1.2.0 assigns this criterion to all missense variants in PALB2, given that PALB2 has a low rate of functionally impactful missense variants and true pathogenic missense variants are thought to be exceedingly rare.2 In silico predictors are not applied (PP3/BP4 not used for missense variants per VCEP). REVEL score is 0.219 and BayesDel score is 0.039. SpliceAI predicts no splice impact (max delta = 0.00).3 This variant has been reported in ClinVar (ID 410148) as Uncertain Significance by the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer VCEP and by 3 clinical laboratories. No case-control studies, co-segregation data, or functional studies specific to this variant were identified.4 PVS1, PS1, PS3, PM1, PM5, PP2, PP3, PP4, PP5, BS3, BP2, BP4, BP5, BP6, and BP7 are not applicable per PALB2 VCEP v1.2.0 rules, predominantly because missense pathogenic variation is not yet confirmed as a disease mechanism for PALB2. PS2, PS4, PM6, PP1, BA1, BS1, BS2, and BS4 are not met due to absence of qualifying evidence.5 With PM2_Supporting (1 pathogenic supporting criterion) and BP1_Supporting (1 benign supporting criterion) in a VCEP framework with no other met criteria, the evidence is balanced between benign and pathogenic signals. The variant is classified as Uncertain Significance per the ACMG/AMP combining rules (Rule 31: ≥1 benign supporting + ≥1 pathogenic supporting → VUS with conflicting evidence). This is consistent with the ClinGen Expert Panel classification.6

PM2 + BP1 VUS
Gene diagram · NM_024675.3 · variants mapped to exon structure
PALB2 NM_024675.3
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Uncertain Significance by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 410148)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.219. BayesDel score = 0.0388102.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PALB2, a scaffolding protein involved in DNA repair, is altered in various cancers.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      28319063 ↗ Compromised BRCA1-PALB2 interaction is associated with breast cancer risk. ONCOKB
      25741868 ↗ 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. CLINVAR
      34242744 ↗ Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
      18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
      20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR
      24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR