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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, a gene in which primarily truncating variants are known to cause disease and missense pathogenic variation is not yet confirmed as a disease mechanism (VCEP v1.2.0).

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, a gene in which primarily truncating variants are known to cause disease and missense pathogenic variation is not yet confirmed as a disease mechanism (VCEP v1.2.0).1 The variant is present in gnomAD v4.1 at an overall allele frequency of 0.01276% (206/1,614,002 alleles, 0 homozygotes) with a grpmax filtering AF of 0.015106% in the European (non-Finnish) population. This exceeds the PALB2 VCEP BS1 threshold of >0.01%, supporting a benign interpretation at Strong strength.2 SpliceAI predicts no significant splice impact (max delta score = 0.02), consistent with a missense change without cryptic splice effects.3 REVEL score is 0.034 and BayesDel score is -0.732, consistent with a benign in silico profile, though computational predictors have not been validated for PALB2 missense variant functional outcome per the VCEP.4 BP1 (Supporting) is applied per the PALB2 VCEP, which assigns this code to all missense variants given the very low prior probability that PALB2 missense variants are pathogenic.5 Combining BS1 (Strong benign) with BP1 (Supporting benign) yields a classification of Likely Benign per the ACMG/AMP combination rules adopted by the PALB2 VCEP (Rule 20: ≥1 Benign Strong criterion).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
      Population frequency
      Overall AF
      206 / 1,614,002
      0.013%
      Highest · European (non-Finnish)
      0.017%
      Homozygotes
      0
      grpmax FAF
      0.015%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 201 / 1,179,992 0.017% 0
      Admixed American 0 / 59,996
      European (Finnish) 0 / 64,036
      Amish 0 / 912
      East Asian 0 / 44,894
      Middle Eastern 0 / 6,084
      South Asian 0 / 91,078
      Ashkenazi Jewish 0 / 29,602
      African/African American 0 / 74,928
      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.
      Overall AF
      12 / 251,176
      0.0048%
      Highest · European (non-Finnish)
      0.011%
      Homozygotes
      0
      grpmax FAF
      0.006%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 12 / 113,616 0.011% 0
      African/African American 0 / 16,190
      Admixed American 0 / 34,564
      Ashkenazi Jewish 0 / 10,078
      East Asian 0 / 18,394
      European (Finnish) 0 / 21,620
      Remaining individuals 0 / 6,116
      South Asian 0 / 30,598
      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.
      This variant is absent from gnomAD-Canada.
      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.
      Literature · 22 PMIDs triaged · 8 high-priority
      22papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      26467025 ↗ functional
      A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
      We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies
      BS3PS3PS4
      26635394 ↗ functional
      RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins.
      Transcription factors bind to the genome by forming specific contacts with the primary DNA sequence; however, RNA-binding proteins (RBPs) have greater scope to achieve binding specificity through the RNA secondary structure. It has been revealed that single nucleotide variants (SNVs) that alter RNA structure, also known as RiboSNitches, exhibit 3-fold greater local structure changes than replicate
      BS3PP5PS3PS4
      15604628 ↗ case observation
      Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Cancer Genetic Counseling Special Interest Group. The information contained in
      PP5PS4
      17200668 ↗ case observation
      PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene.
      PALB2 interacts with BRCA2, and biallelic mutations in PALB2 (also known as FANCN), similar to biallelic BRCA2 mutations, cause Fanconi anemia. We identified monoallelic truncating PALB2 mutations in 10/923 individuals with familial breast cancer compared with 0/1,084 controls (P = 0.0004) and show that such mutations confer a 2.3-fold higher risk of breast cancer (95% confidence interval (c.i.) =
      PP5PS4
      17508274 ↗ case observation
      Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial and ethical implications of identifying at-risk individuals for hereditary breast and ovarian cancer (HBOC) through cancer risk assessment, with or without genetic susceptibility testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors' Familial Cancer
      PP5PS4
      18163131 ↗ case observation
      The emerging landscape of breast cancer susceptibility.
      The genetic basis of inherited predisposition to breast cancer has been assiduously investigated for the past two decades and has been the subject of several recent discoveries. Three reasonably well-defined classes of breast cancer susceptibility alleles with different levels of risk and prevalence in the population have become apparent: rare high-penetrance alleles, rare moderate-penetrance alle
      PP5PS4
      20301425 ↗ case observation
      Untitled reference
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PS3PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots