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PALB2
Final classification
VUS
PALB2 c.1960A>G · p.Ile654Val
PALB2

The PALB2 c.1960A>G (p.Ile654Val) variant has been reported in ClinVar with predominantly uncertain significance submissions and one likely benign submission, and no expert panel classification was identified.

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.1960A>G
Consequence
N/A
GRCh38
chr16:23630194 T>C
GRCh37
chr16:23641515 T>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework was evaluated deterministically with applied criteria: BP1 supporting; 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; no rule matched the adjudicated criteria.
Classification rationale
BP1 VUS
PALB2 c.1960A>G

The PALB2 c.1960A>G (p.Ile654Val) variant has been reported in ClinVar with predominantly uncertain significance submissions and one likely benign submission, and no expert panel classification was identified.1 This variant is present in gnomAD v4 at 0.00043% overall (7/1,614,140 alleles) with a highest observed population frequency of 0.00769% in South Asians, which is above the PALB2 PM2_Supporting threshold of 0.000333% and below the BS1 threshold of 0.01%.2 Under the PALB2 expert specification, BP1 is met because this is a missense variant in a gene for which established pathogenic variation is predominantly truncating.3 SpliceAI predicts no significant splice impact for this variant (maximum delta score 0.01); REVEL is 0.043 and BayesDel is -0.826097, although the PALB2 expert specification does not use PP3 or BP4 for missense prediction alone.4

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= 4.33667e-06; MAF= 0.00043%, 7/1614140 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 7.68521e-05; MAF= 0.00769%, 7/91084 alleles, homozygotes = 0); grpmax FAF= 3.587e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.96324e-06; MAF= 0.00080%, 2/251154 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 6.53296e-05; MAF= 0.00653%, 2/30614 alleles, homozygotes = 0); grpmax FAF= 1.082e-05.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00043% · 7 / 1,614,140
      0 hom · FAF 0.0036%
      South Asian
      7 / 91,084
      0.0077%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      0.0008% · 2 / 251,154
      0 hom · FAF 0.0011%
      South Asian
      2 / 30,614
      0.0065%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (8 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 234115)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.043. BayesDel score = -0.826097.
      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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 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
      27648926 ↗ Whole-exome sequencing and targeted gene sequencing provide insights into the role of PALB2 as a male breast cancer susceptibility gene. 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
      21279724 ↗ Mutations in Fanconi anemia genes and the risk of esophageal cancer. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR