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PALB2
Final classification
Benign
PALB2 c.721A>G · p.Asn241Asp
PALB2

The PALB2 c.721A>G (p.Asn241Asp) missense variant has an allele frequency of 0.63% in the African/African American population in gnomAD v4.1 (472/75,032 alleles) with 3 homozygous individuals observed. The grpmax filtering allele frequency of 0.58% exceeds the PALB2 VCEP BA1 threshold of >0.1%, meeting stand-alone benign criteria.

Gene
PALB2
Transcript
NM_024675.3
HGVS · transcript:coding
NM_024675.3:c.721A>G
Consequence
N/A
GRCh38
chr16:23635825 T>C
GRCh37
chr16:23647146 T>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule17 (1 Benign.Stand Alone) with applied criteria: BA1 stand-alone benign, BS1 strong benign, BP1 supporting benign, BP6 supporting benign; maps to Benign.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule17 (1 Benign.Stand Alone) with applied criteria: BA1 stand-alone benign, BS1 strong benign, BP1 supporting benign, BP6 supporting benign; maps to Benign.
Classification rationale
BA1BS1BP1BP6 Benign
PALB2 c.721A>G

The PALB2 c.721A>G (p.Asn241Asp) missense variant has an allele frequency of 0.63% in the African/African American population in gnomAD v4.1 (472/75,032 alleles) with 3 homozygous individuals observed. The grpmax filtering allele frequency of 0.58% exceeds the PALB2 VCEP BA1 threshold of >0.1%, meeting stand-alone benign criteria.1 The grpmax filtering allele frequency of 0.58% in gnomAD v4.1 far exceeds the PALB2 VCEP BS1 threshold of >0.01%, providing strong benign evidence. This allele frequency is inconsistent with a highly penetrant pathogenic variant for PALB2-related cancer predisposition.2 BP1 (supporting benign) is met per PALB2 VCEP v1.2.0, which applies to all PALB2 missense variants given that true missense pathogenic variants are thought to be exceedingly rare in this gene based on published and unpublished functional studies.3 This variant has been classified as Benign by the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel (expert panel review) and is reported as Benign by 9 clinical laboratories and Likely benign by 8 clinical laboratories in ClinVar (VariationID: 126765).4 SpliceAI predicts no splice impact (max delta score 0.00). REVEL score is 0.013 and BayesDel score is -0.834, consistent with a benign in silico profile, though these predictors are not used for PALB2 missense variants per VCEP guidance.5 PVS1, PS1, PS3, PM1, PP2, and PP3 are not applicable to this missense variant per PALB2 VCEP v1.2.0. PS4, PM2, PP1, and BS4 are not met due to absence of required evidence. Full-text verification of cited publications was attempted but the retrieved full-text files contained only Sci-Hub interface content rather than actual paper text; citation verification was limited to abstracts.6 Applying the PALB2 VCEP v1.2.0 final classification rules: BA1 (stand-alone benign) is met, which alone satisfies Rule 17 (>=1 Stand Alone Benign) for a Benign classification. Additionally, BS1 (strong benign) and BP1 (supporting benign) are met, further supporting the benign interpretation.7

BA1 + BS1 + BP1 + BP6 Benign
5 spliceai ↗revelbayesdel
7 cspec ↗final_classification_framework
Gene diagram · NM_024675.3 · variants mapped to exon structure
PALB2 NM_024675.3
Fetching transcript structure from UCSC…
Applied criteria · 4 applied · 5 assessed
Applied · 4
Strength Supporting Moderate Strong Very strong
BA1 stand-alone Benign
The grpmax filtering allele frequency in gnomAD v4.1 is 0.58% (FAF 0.00582118), which exceeds the PALB2 VCEP BA1 threshold of >0.1%. This allele frequency is inconsistent with a highly penetrant pathogenic variant for PALB2-related cancer predisposition and meets stand-alone benign criteria.
gnomAD v4.1: grpmax FAF 0.00582118 (0.58%)derived from African/African American subpopulation AF 0.629% (472/75032 alleles
BS1 strong Benign
The grpmax filtering allele frequency in gnomAD v4.1 is 0.58% (FAF 0.00582118), which far exceeds the PALB2 VCEP BS1 threshold of >0.01%. The variant is common in the African/African American population (AF 0.63%) with 3 homozygous individuals observed in gnomAD v4.1, providing strong evidence for a benign interpretation.
gnomAD v4.1: grpmax FAF 0.58% > 0.01% VCEP BS1 thresholdAfrican/African American subpopulation AF 0.63% (472/75032 alleles
BP1 supporting Benign
BP1 applies to all PALB2 missense variants per VCEP guidance: true missense pathogenic variants are thought to be exceedingly rare in PALB2, which has a low rate of non-functional missense variants in relevant assays. This variant is a missense change (p.Asn241Asp).
PALB2 VCEP v1.2.0: BP1 'Apply to all missense variants' with supporting strengthbased on published and unpublished functional studies showing low rate of non-functional PALB2 missense variants.
BP6 supporting Benign
Expert panel ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen classified as Benign.
PALB2 VCEP v1.2.0: BP6 'Not Applicable for this VCEP'.ClinVar expert panel classification
Assessed · not applied
Pathogenic
PS4 No case-control study meeting PALB2 VCEP PS4 thresholds (p-value <= 0.05 AND odds ratio >= 3 OR lower 95% CI >= 1.5) has been identified for this variant.
PM2 The allele frequency in gnomAD v4.1 is 0.03327% (537/1,614,164 alleles), which far exceeds the PALB2 VCEP PM2_Supporting threshold of <=0.000333% (<=1/300,000).
PP1 No co-segregation data meeting PALB2 VCEP PP1 thresholds (LOD >= 0.3 or Bayes Factor >= 2:1 for AD condition) has been identified.
Benign
BS2 BS2 per PALB2 VCEP requires Fanconi Anemia proband data scored via VCEP BS2 tables and explicitly excludes population cohort data such as gnomAD.
BS4 No quantitative co-segregation analysis meeting PALB2 VCEP BS4 thresholds (LOD <= -1.28 for Strong, LOD <= -0.64 for Moderate, LOD <= -0.32 for Supporting) has been identified.
N/A · 16 PVS1 · PS1 · PS2 · PS3 · PM1 · PM5 · PM6 · PP2 · PP3 · PP4 · PP5 · BS3 · BP2 · BP4 · BP5 · BP7
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= 0.00033268; MAF= 0.03327%, 537/1614164 alleles, homozygotes = 3) and has highest observed frequency in the African/African American population (AF= 0.00629065; MAF= 0.62906%, 472/75032 alleles, homozygotes = 3); grpmax FAF= 0.00582118.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.000615807; MAF= 0.06158%, 174/282556 alleles, homozygotes = 2) and has highest observed frequency in the African/African American population (AF= 0.00652699; MAF= 0.65270%, 162/24820 alleles, homozygotes = 2); grpmax FAF= 0.00550914.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.033% · 537 / 1,614,164
3 hom · FAF 0.58%
African/African American
472 / 75,032
0.63%
3 hom
Remaining individuals
33 / 62,508
0.053%
Admixed American
18 / 60,014
0.03%
European (non-Finnish)
14 / 1,180,034
0.0012%
+ 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
0.062% · 174 / 282,556
2 hom · FAF 0.55%
African/African American
162 / 24,820
0.65%
2 hom
Remaining individuals
2 / 7,202
0.028%
Admixed American
9 / 35,436
0.025%
European (non-Finnish)
1 / 129,044
0.00077%
+ 4 not observed (Ashkenazi Jewish, East Asian, European (Finnish), 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 Benign (9 clinical laboratories) and as Likely benign (8 clinical laboratories) and as Benign by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 126765)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.013. BayesDel score = -0.834201.
Functional / OncoKB screenshot
Functional Inconclusive
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Inconclusive; curated oncogenicity label: Inconclusive.
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; COSV104552978, 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 · 8 PMIDs not cited in assessment
21932393 ↗ Novel germline PALB2 truncating mutations in African American breast cancer patients. ONCOKB
21113654 ↗ Germline mutations in PALB2 in African-American breast cancer cases. CLINVAR
23918944 ↗ Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. CLINVAR
25356972 ↗ BRCA1, BRCA2, PALB2, and CDKN2A mutations in familial pancreatic cancer: a PACGENE study. CLINVAR
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
33964450 ↗ A Validated Functional Analysis of Partner and Localizer of BRCA2 Missense Variants for Use in Clinical Variant Interpretation. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR