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PALB2
Final classification
VUS
PALB2 c.740C>G · p.Thr247Arg
PALB2

NM_024675.4:c.740C>G (p.Thr247Arg) is a missense variant in exon 4 of PALB2 identified in 1 of 1996 Australian familial breast cancer cases and 0 of 1998 cancer-free controls (Thompson et al. 2015).

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.740C>G
Consequence
N/A
GRCh38
chr16:23635806 G>C
GRCh37
chr16:23647127 G>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework was evaluated deterministically with applied criteria: BP1 supporting benign; 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 benign; no rule matched the adjudicated criteria.
Classification rationale
BP1 VUS
PALB2 c.740C>G

NM_024675.4:c.740C>G (p.Thr247Arg) is a missense variant in exon 4 of PALB2 identified in 1 of 1996 Australian familial breast cancer cases and 0 of 1998 cancer-free controls (Thompson et al. 2015).1 Under the ClinGen PALB2 VCEP v1.2.0 framework, most pathogenic criteria are not applicable to missense variants: PVS1 (null variant only), PS1 (missense excluded), PM1 (missense excluded), PM5 (truncating only), PP2 (missense excluded), PP3/BP4 (missense excluded). PS3/BS3 are not applicable per VCEP.2 BP1_Supporting is met: the PALB2 VCEP applies BP1 to all missense variants at Supporting level, reflecting the very low likelihood that missense variants in PALB2 are pathogenic based on published functional data.3 PM2 could not be assessed: gnomAD v4 frequency data is unavailable (scrape timed out). The variant has an rsID (rs587782658) and is present in population databases, but the exact allele frequency needed for the VCEP PM2_Supporting threshold (≤0.000333%) requires manual confirmation. PS4 is not met: the single case observation (1/1996 cases vs 0/1998 controls) does not constitute a statistically significant case-control enrichment (p=0.48, Fisher's exact test).4 No functional data (PS3 not applicable per VCEP), no segregation data (PP1/BS4 not assessed), no de novo reports (PS2/PM6 not applicable), and no Fanconi Anemia observations (BS2 not assessed) are available for this variant. In silico predictors are mixed: REVEL score 0.065 and BayesDel -0.512 are benign-leaning; SpliceAI delta 0.00 predicts no splice impact. However, under VCEP rules, PP3 and BP4 are not applicable for missense variants regardless of predictor scores.5 ClinVar classification is Uncertain significance (7 clinical laboratories) / Likely benign (1 laboratory), with no expert panel review. This is consistent with the limited evidence available for this missense variant.6

BP1 VUS
Gene diagram · NM_024675.4 · variants mapped to exon structure
PALB2 NM_024675.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 8 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP1 supporting Benign
PALB2 VCEP v1.2.0: 'Apply to all missense variants' at Supporting strength. Based on published and unpublished functional studies, PALB2 has a low rate of missense variants that are non-functional in relevant assays; true missense pathogenic variants are thought to be exceedingly rare. This missense variant (p.Thr247Arg) is eligible for BP1_Supporting.
VCEP BP1 rule: applicable to all PALB2 missense variants at Supporting level.
Assessed · not applied
Pathogenic
PS4 The variant was observed in 1 of 1996 familial breast cancer cases and 0 of 1998 controls in Thompson et al.
PM2 PALB2 VCEP PM2_Supporting requires frequency ≤0.000333% in gnomAD v4.
PP1 No co-segregation data or family studies evaluating NM_024675.4:c.740C>G were identified in the literature or evidence packet.
Benign
BA1 PALB2 VCEP BA1 requires Grpmax Filtering AF >0.1% in gnomAD v4.
BS1 PALB2 VCEP BS1 requires Grpmax Filtering AF >0.01% in gnomAD v4.
BS2 PALB2 VCEP BS2 requires Fanconi Anemia proband scoring.
BS4 No co-segregation or family study data available for this variant.
BP7 PALB2 VCEP BP7 applies to synonymous variants and deep intronic variants (beyond +7 donor / -21 acceptor).
N/A · 17 PVS1 · PS1 · PS2 · PS3 · PM1 · PM5 · PM6 · PP2 · PP3 · PP4 · PP5 · BS3 · BP2 · BP3 · BP4 · BP5 · BP6
Research & evidence
Population frequency
v4.1
This variant is absent from gnomAD v4.1.
v2.1
This variant is absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
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 (7 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 142706)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.065. BayesDel score = -0.511995.
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
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 8 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
28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. 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
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
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
26283626 ↗ Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls. CLINVAR
26315354 ↗ Germline Mutations in the BRIP1, BARD1, PALB2, and NBN Genes in Women With Ovarian Cancer. CLINVAR