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PALB2
Final classification
VUS
PALB2 c.1042C>A · p.Gln348Lys
PALB2

The PALB2 c.1042C>A (p.Gln348Lys; Q348K) variant has been reported in ClinVar with predominantly uncertain significance submissions, with additional likely benign and benign submissions.

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.1042C>A
Consequence
N/A
GRCh38
chr16:23635504 G>T
GRCh37
chr16:23646825 G>T
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.1042C>A

The PALB2 c.1042C>A (p.Gln348Lys; Q348K) variant has been reported in ClinVar with predominantly uncertain significance submissions, with additional likely benign and benign submissions.1 This variant is present in gnomAD v4.1 at an overall allele frequency of 0.00304% (49/1,613,732 alleles) with a highest observed population frequency of 0.00415% in European non-Finnish individuals; this is below the PALB2 BS1 threshold of 0.01% and above the PM2 threshold of 0.000333%.2 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.00, which is below the PALB2 PP3 splicing threshold of 0.2.3 Because this is a PALB2 missense variant, BP1 is met at supporting strength under the PALB2 specification, while PVS1 is not met because the variant is not a truncating or canonical splice-site loss-of-function change.4

BP1 VUS
4 cspec ↗pvs1_variant_assessmentpvs1_gene_context
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= 3.03644e-05; MAF= 0.00304%, 49/1613732 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.15285e-05; MAF= 0.00415%, 49/1179912 alleles, homozygotes = 0); grpmax FAF= 3.179e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.89383e-05; MAF= 0.00389%, 11/282498 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.52832e-05; MAF= 0.00853%, 11/128982 alleles, homozygotes = 0); grpmax FAF= 4.742e-05.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.003% · 49 / 1,613,732
      0 hom · FAF 0.0032%
      European (non-Finnish)
      49 / 1,179,912
      0.0042%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0039% · 11 / 282,498
      0 hom · FAF 0.0047%
      European (non-Finnish)
      11 / 128,982
      0.0085%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (9 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Benign (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.02. BayesDel score = -0.53199.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: 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