Starting
Initialising…
0%
PALB2
Final classification
Uncertain Significance - Conflicting Evidence
PALB2 c.1351T>G · p.Leu451Val
PALB2

This variant is a missense change (NM_024675.4:c.1351T>G, p.Leu451Val) in PALB2, a gene where loss of function is a known disease mechanism for PALB2-related cancer predisposition (autosomal dominant) and Fanconi anemia type FA-N (autosomal recessive).

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.1351T>G
Consequence
N/A
GRCh38
chr16:23635195 A>C
GRCh37
chr16:23646516 A>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP1 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP1 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP1 Uncertain Significance - Conflicting Evidence
PALB2 c.1351T>G

This variant is a missense change (NM_024675.4:c.1351T>G, p.Leu451Val) in PALB2, a gene where loss of function is a known disease mechanism for PALB2-related cancer predisposition (autosomal dominant) and Fanconi anemia type FA-N (autosomal recessive).1 In gnomAD v4.1, the variant is present at extremely low frequency (AF = 0.00031%, 5/1,614,074 alleles; grpmax FAF = 7.9e-07), meeting the PALB2 VCEP PM2_Supporting threshold (≤0.000333%).2 BP1_Supporting is applied per PALB2 VCEP rule: all missense variants in PALB2 receive BP1 because missense pathogenic variation is not yet confirmed as a disease mechanism and true pathogenic missense variants are thought to be exceedingly rare.3 SpliceAI predicts no splicing impact (max delta = 0.00), and REVEL (0.027) and BayesDel (-0.741) scores are consistent with a benign in silico profile, though PP3 and BP4 are not applied to missense variants per VCEP rules.4 The variant has been observed in COSMIC in 2 somatic cancer samples but has no curated functional evidence from OncoKB.5 ClinVar reports this variant as Uncertain significance (VariationID 951843, 2 clinical laboratories, criteria provided single submitter) with no expert panel classification.6 No published literature specifically mentions NM_024675.4:c.1351T>G; all 16 PMIDs retrieved through ClinVar and literature searches were reviewed and none contain variant-specific evidence. All available full-text papers (PMID:34242744, 15604628, 17508274, 18163131) were confirmed to not mention this variant. No co-segregation data, case-control studies, de novo reports, or functional studies are available for this variant. PS4, PP1, BS2, BS4, and PVS1 remain not assessed due to absence of evidence. The only criteria met are PM2_Supporting (low population frequency) and BP1_Supporting (missense in PALB2). This yields a net of one pathogenic supporting and one benign supporting criterion — insufficient for classification beyond VUS per ACMG/AMP combination rules. The variant remains Uncertain significance.7

PM2 + BP1 Uncertain Significance - Conflicting Evidence
Gene diagram · NM_024675.4 · variants mapped to exon structure
PALB2 NM_024675.4
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
      This variant is present in gnomAD v4.1 (AF= 3.09775e-06; MAF= 0.00031%, 5/1614074 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66639e-05; MAF= 0.00167%, 1/60010 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.19887e-05; MAF= 0.00120%, 3/250236 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89352e-05; MAF= 0.00289%, 1/34560 alleles, homozygotes = 0); grpmax FAF= 2.94e-06.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00031% · 5 / 1,614,074
      0 hom · FAF 7.9e-05%
      Admixed American
      1 / 60,010
      0.0017%
      European (non-Finnish)
      4 / 1,180,002
      0.00034%
      + 8 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0012% · 3 / 250,236
      0 hom · FAF 0.00029%
      Admixed American
      1 / 34,560
      0.0029%
      European (non-Finnish)
      2 / 112,958
      0.0018%
      + 6 not observed (African/African 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 (2 clinical laboratories). (ClinVarID = 951843)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.027. BayesDel score = -0.741444.
      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 previously been reported in somatic cancers (COSMIC; COSV55167320, n = 2 times).
      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
      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
      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
      24432435 ↗ PMID:24432435 CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR