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PALB2
Final classification
Uncertain Significance - Conflicting Evidence
PALB2 c.1351T>G · p.Leu451Val
PALB2

This variant is a missense change (NM_024675.4:c.1351T>G, p.Leu451Val) in PALB2, a gene where loss of function is a known disease mechanism for PALB2-related cancer predisposition (autosomal dominant) and Fanconi anemia type FA-N (autosomal recessive).

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.1351T>G
Consequence
N/A
GRCh38
chr16:23635195 A>C
GRCh37
chr16:23646516 A>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP1 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP1 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP1 Uncertain Significance - Conflicting Evidence
PALB2 c.1351T>G

This variant is a missense change (NM_024675.4:c.1351T>G, p.Leu451Val) in PALB2, a gene where loss of function is a known disease mechanism for PALB2-related cancer predisposition (autosomal dominant) and Fanconi anemia type FA-N (autosomal recessive).1 In gnomAD v4.1, the variant is present at extremely low frequency (AF = 0.00031%, 5/1,614,074 alleles; grpmax FAF = 7.9e-07), meeting the PALB2 VCEP PM2_Supporting threshold (≤0.000333%).2 BP1_Supporting is applied per PALB2 VCEP rule: all missense variants in PALB2 receive BP1 because missense pathogenic variation is not yet confirmed as a disease mechanism and true pathogenic missense variants are thought to be exceedingly rare.3 SpliceAI predicts no splicing impact (max delta = 0.00), and REVEL (0.027) and BayesDel (-0.741) scores are consistent with a benign in silico profile, though PP3 and BP4 are not applied to missense variants per VCEP rules.4 The variant has been observed in COSMIC in 2 somatic cancer samples but has no curated functional evidence from OncoKB.5 ClinVar reports this variant as Uncertain significance (VariationID 951843, 2 clinical laboratories, criteria provided single submitter) with no expert panel classification.6 No published literature specifically mentions NM_024675.4:c.1351T>G; all 16 PMIDs retrieved through ClinVar and literature searches were reviewed and none contain variant-specific evidence. All available full-text papers (PMID:34242744, 15604628, 17508274, 18163131) were confirmed to not mention this variant. No co-segregation data, case-control studies, de novo reports, or functional studies are available for this variant. PS4, PP1, BS2, BS4, and PVS1 remain not assessed due to absence of evidence. The only criteria met are PM2_Supporting (low population frequency) and BP1_Supporting (missense in PALB2). This yields a net of one pathogenic supporting and one benign supporting criterion — insufficient for classification beyond VUS per ACMG/AMP combination rules. The variant remains Uncertain significance.7

PM2 + BP1 Uncertain Significance - Conflicting Evidence
Gene diagram · NM_024675.4 · variants mapped to exon structure
PALB2 NM_024675.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 7 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is present at extremely low frequency in gnomAD v4.1 (AF = 0.00031%, 5/1,614,074 alleles), which is at or below the PALB2 VCEP PM2_Supporting threshold of ≤0.000333% (≤1/300,000). Applied as PM2_Supporting per VCEP guidance.
gnomAD v4.1: AF = 0.00031% (5/1614074)
BP1 supporting Benign
PALB2 VCEP v1.2.0 BP1 rule states: 'Apply to all missense variants.' This variant is a missense change (p.Leu451Val) in PALB2, a gene where primarily truncating variants are known to cause disease and missense pathogenic variants are thought to be exceedingly rare.
PALB2 VCEP BP1 rule applies to all missense variants in PALB2PALB2 has a low rate of missense variants that are non-functional in relevant assays
Assessed · not applied
Pathogenic
PVS1 PVS1 is not applicable to this missense variant (p.Leu451Val) per the PALB2 VCEP v1.2.0 PVS1 Decision Tree.
PS4 No case-control study or cohort analysis demonstrating statistically increased prevalence of NM_024675.4:c.1351T>G in affected individuals has been identified.
PP1 No co-segregation data are available for this variant.
Benign
BA1 gnomAD v4.1 grpmax filtering allele frequency is 7.9e-07 (0.000079%), far below the PALB2 VCEP BA1 threshold of >0.1%.
BS1 gnomAD v4.1 grpmax filtering allele frequency is 7.9e-07 (0.000079%), far below the PALB2 VCEP BS1 threshold of >0.01%.
BS2 No evidence of the variant observed in healthy adult individuals for a recessive (Fanconi anemia) disorder context.
BS4 No segregation data demonstrating lack of co-segregation of this variant with disease in affected family members are available.
N/A · 17 PS1 · PS2 · PS3 · PM1 · PM5 · PM6 · PP2 · PP3 · PP4 · PP5 · BS3 · BP2 · BP3 · BP4 · BP5 · BP6 · BP7
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= 3.09775e-06; MAF= 0.00031%, 5/1614074 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66639e-05; MAF= 0.00167%, 1/60010 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.19887e-05; MAF= 0.00120%, 3/250236 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89352e-05; MAF= 0.00289%, 1/34560 alleles, homozygotes = 0); grpmax FAF= 2.94e-06.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031% · 5 / 1,614,074
0 hom · FAF 7.9e-05%
Admixed American
1 / 60,010
0.0017%
European (non-Finnish)
4 / 1,180,002
0.00034%
+ 8 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0012% · 3 / 250,236
0 hom · FAF 0.00029%
Admixed American
1 / 34,560
0.0029%
European (non-Finnish)
2 / 112,958
0.0018%
+ 6 not observed (African/African 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 (2 clinical laboratories). (ClinVarID = 951843)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.027. BayesDel score = -0.741444.
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; COSV55167320, n = 2 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
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
24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR
24366402 ↗ Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force. CLINVAR
24432435 ↗ PMID:24432435 CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR