Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
PALB2
Final classification
VUS
PALB2 c.3044C>T · p.Thr1015Ile
PALB2

NM_024675.4:c.3044C>T (p.Thr1015Ile) is a missense variant in PALB2, a gene in which loss-of-function is an established mechanism for autosomal dominant hereditary breast, ovarian, and pancreatic cancer predisposition.

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.3044C>T
Consequence
N/A
GRCh38
chr16:23621431 G>A
GRCh37
chr16:23632752 G>A
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework was evaluated deterministically with applied criteria: 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: BP1 supporting benign; no rule matched the adjudicated criteria.
Classification rationale
BP1 VUS
PALB2 c.3044C>T

NM_024675.4:c.3044C>T (p.Thr1015Ile) is a missense variant in PALB2, a gene in which loss-of-function is an established mechanism for autosomal dominant hereditary breast, ovarian, and pancreatic cancer predisposition.1 This variant is present in gnomAD v4.1 at a total allele frequency of 0.00099% (16/1,614,014 alleles; grpmax FAF 0.000803%), predominantly in the European (non-Finnish) subpopulation. It is also present in gnomAD v2.1 at 0.00119% (3/251,446 alleles) and is absent from gnomAD-Canada.2 This variant has been reported in ClinVar as Uncertain significance by 6 clinical laboratories and as Likely benign by 1 laboratory (ClinVar Variation ID 141554). No expert panel classifications are available.3 In silico predictors yield mixed results: REVEL score 0.238 (below the 0.5 threshold commonly used for deleterious prediction), BayesDel score -0.308 (below the 0.0 threshold for benign prediction), and SpliceAI max delta 0.00 (no predicted splicing impact).4 PALB2 VCEP BP1_Supporting is met: this criterion applies to all missense variants in PALB2 because true pathogenic missense variants are thought to be exceedingly rare, per the ClinGen HBOP VCEP v1.2.0.5 PALB2 VCEP PM2_Supporting is not met: the variant frequency in gnomAD v4 (0.00099%) exceeds the VCEP threshold of ≤0.000333%. BS1 and BA1 are also not met as the grpmax FAF (0.000803%) does not exceed either the BS1 (>0.01%) or BA1 (>0.1%) thresholds.6 Multiple PALB2 VCEP criteria are not applicable to missense variants by explicit VCEP rule: PVS1 (not a null variant), PS1, PM1, PM5, PP2, PP3, BP4, BP7. Additionally, PS2, PS3, PM6, PP4, PP5, BP2, BP3, BP5, BP6 are not applicable per VCEP framework.7 PS4, PP1, BS2, and BS4 could not be assessed due to absence of variant-specific case-control, segregation, or Fanconi Anemia proband data in the evidence reviewed. No reviewed publication (10 PMIDs screened, 5 full-text papers read) mentioned NM_024675.4:c.3044C>T. None of the ClinVar-submitted PMIDs contained variant-specific evidence for this missense.8 With only BP1_Supporting (supporting benign) met and no pathogenic criteria met, this variant is classified as Uncertain Significance (VUS) per ACMG/AMP 2015 combining rules. The single supporting benign criterion is insufficient for Likely Benign classification, which requires ≥2 supporting benign criteria or 1 strong benign + 1 supporting benign.9

BP1 VUS
Gene diagram · NM_024675.4 · variants mapped to exon structure
PALB2 NM_024675.4
Fetching transcript structure from UCSC…
Applied criteria · 1 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
      This variant is present in gnomAD v4.1 (AF= 9.91317e-06; MAF= 0.00099%, 16/1614014 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.35593e-05; MAF= 0.00136%, 16/1180006 alleles, homozygotes = 0); grpmax FAF= 8.03e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.1931e-05; MAF= 0.00119%, 3/251446 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.63764e-05; MAF= 0.00264%, 3/113738 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00099% · 16 / 1,614,014
      0 hom · FAF 0.0008%
      European (non-Finnish)
      16 / 1,180,006
      0.0014%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0012% · 3 / 251,446
      0 hom · FAF 0.0007%
      European (non-Finnish)
      3 / 113,738
      0.0026%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      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 (6 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 141554)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.238. BayesDel score = -0.308316.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      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
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      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
      28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. 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
      17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
      24366402 ↗ Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force. CLINVAR
      25085752 ↗ Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. CLINVAR
      31479213 ↗ PMID 31479213 CLINVAR
      33471991 ↗ Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. CLINVAR