Starting
Initialising…
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PALB2
Final classification
Likely Benign
PALB2 c.928A>G · p.Ser310Gly
PALB2

NM_024675.4:c.928A>G (p.Ser310Gly) is a missense variant in PALB2 exon 4. Under the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel specifications for PALB2 v1.2.0, missense pathogenic variation is not yet confirmed as a mechanism of disease.

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.928A>G
Consequence
N/A
GRCh38
chr16:23635618 T>C
GRCh37
chr16:23646939 T>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule18 (1 Benign.Strong + 1 Benign.Supporting) with applied criteria: BS1 strong, BP1 supporting benign; maps to Likely Benign.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule18 (1 Benign.Strong + 1 Benign.Supporting) with applied criteria: BS1 strong, BP1 supporting benign; maps to Likely Benign.
Classification rationale
BS1BP1 Likely Benign
PALB2 c.928A>G

NM_024675.4:c.928A>G (p.Ser310Gly) is a missense variant in PALB2 exon 4. Under the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel specifications for PALB2 v1.2.0, missense pathogenic variation is not yet confirmed as a mechanism of disease.1 The variant is present in gnomAD v4.1 at a grpmax filtering allele frequency of 0.01511% (206/1,614,002 alleles), exceeding the PALB2 VCEP BS1 threshold of >0.01%, meeting BS1 at Strong strength.2 BP1 (Supporting benign) is met per VCEP rule that applies to all PALB2 missense variants, as true missense pathogenic variants in PALB2 are thought to be exceedingly rare.3 The gnomAD v4.1 frequency (0.01511%) does not reach the BA1 threshold (>0.1%) or the PM2 threshold (<=0.000333%). In silico predictions (SpliceAI max delta=0.02, REVEL=0.034, BayesDel=-0.732) are not used under this VCEP for missense variants per PP3/BP4 rules.4 No case-control studies, co-segregation data, or Fanconi Anemia biallelic observations were available to assess PS4, PP1, BS2, or BS4.5 Applying the PALB2 VCEP/ACMG combination rules: one Benign Strong criterion (BS1) plus one Benign Supporting criterion (BP1) is consistent with a Likely Benign classification per Rule 18.6

BS1 + BP1 Likely Benign
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 · supports benign
      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= 0.000127633; MAF= 0.01276%, 206/1614002 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00017034; MAF= 0.01703%, 201/1179992 alleles, homozygotes = 0); grpmax FAF= 0.00015106.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.77753e-05; MAF= 0.00478%, 12/251176 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000105619; MAF= 0.01056%, 12/113616 alleles, homozygotes = 0); grpmax FAF= 6.019e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.013% · 206 / 1,614,002
      0 hom · FAF 0.015%
      European (non-Finnish)
      201 / 1,179,992
      0.017%
      Remaining individuals
      5 / 62,480
      0.008%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0048% · 12 / 251,176
      0 hom · FAF 0.006%
      European (non-Finnish)
      12 / 113,616
      0.011%
      + 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 (8 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 128149)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.034. BayesDel score = -0.732133.
      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; COSV55167149, n = 1 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
      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
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      26635394 ↗ RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      17200668 ↗ PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. 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 ↗ PMID:20301425 CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR