Variant classification summary

NM_024675.3:c.1684+1G>A

PALB2 · NP_078951.2:p.? · NM_024675.3

GRCh37: chr16:23646182 C>T · GRCh38: chr16:23634861 C>T

Gene: PALB2 Transcript: NM_024675.3

Final call

Pathogenic

PVS1 very strong PM2 supporting PM5 supporting

Variant details

Gene

PALB2

Transcript

NM_024675.3

Protein

NP_078951.2:p.?

gnomAD AF

ClinVar

Uncertain Significance

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_024675.3:c.1684+1G>A is a canonical +1 donor splice site variant in intron 4 of PALB2, a gene for which loss of function is an established mechanism for hereditary breast, ovarian, and pancreatic cancer predisposition (ClinGen PALB2 VCEP v1.2.0).

2

This variant is absent from gnomAD v2.1 and v4.1 population databases, satisfying the PALB2 VCEP PM2_Supporting threshold of ≤0.000333% allele frequency (PM2_Supporting).

3

RNA analysis performed by Lopez-Perolio et al. (2019, PMID:30890586) confirmed aberrant splicing for c.1684+1G>A, supporting classification as a null variant under the PALB2 VCEP PVS1 decision tree at Very Strong strength (PVS1).

4

The variant introduces a premature termination codon upstream of p.Tyr1183 and is predicted to be NMD-prone; combined with RNA-confirmed splice defect, PM5_Supporting is applied per PALB2 VCEP rules (PM5_Supporting).

5

No benign criteria are met: the variant is not present at significant population frequency (BA1/BS1 not met), SpliceAI predicts a strong splice impact (BP4 not met), the variant is not at a position eligible for BP7, and no evidence of normal splicing or lack of segregation is available.

6

Applying the ACMG/AMP combination rules (Richards et al. 2015) as adopted by the PALB2 VCEP: 1 Pathogenic Very Strong (PVS1) + ≥2 Pathogenic Supporting (PM2_Supporting, PM5_Supporting) yields a classification of Pathogenic under Rule 4.

7

Note: The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer VCEP classifies this variant as Uncertain Significance (ClinVar ID 482029). The discrepancy between the automated adjudication (Pathogenic) and the expert panel classification (VUS) may reflect additional VCEP-specific PVS1 decision tree nuances, PS1 splicing table consultation, or clinical judgment not fully captured in the available evidence materials. Human review by a PALB2 VCEP curator is recommended.

Final determination: Rule4 in the Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Pathogenic.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	NM_024675.3:c.1684+1G>A is a canonical +1 donor splice site variant in PALB2, a gene for which loss of function is an established mechanism for hereditary breast, ovarian, and pancreatic cancer predisposition (monoallelic) and Fanconi anemia subtype FA-N (biallelic). The ClinGen PALB2 VCEP v1.2.0 PVS1 decision tree applies. RNA analysis of this variant has been performed and reported (Lopez-Perolio et al., 2019, PMID:30890586), confirming aberrant splicing. Under the PALB2 VCEP framework, PVS1_VeryStrong is assigned for a canonical splice site variant with observed RNA-level splice defect in a gene where LOF is a known disease mechanism.	cspec pvs1_generic_framework PMID:30890586 pvs1_gene_context pvs1_variant_assessment
PS1	Not assessed	The PALB2 VCEP v1.2.0 PS1 criterion for splicing variants requires use of the PALB2 PS1 Splicing table (referenced to PMID:37352859). This table was not available in the case materials. Without access to the PS1 Splicing table, it cannot be determined whether a different nucleotide change at c.1684+1 (e.g., c.1684+1G>T or c.1684+1G>C) has been classified as pathogenic, which would be required to apply PS1.	cspec
PS2	N/A	The PALB2 VCEP v1.2.0 specifies that PS2 is not applicable for autosomal dominant or autosomal recessive PALB2 conditions, as informative de novo occurrences have not been observed.	cspec
PS3	N/A	The PALB2 VCEP v1.2.0 specifies that PS3 (protein-level functional studies) is not applicable. For RNA-level evidence of splice defects, the VCEP directs use of PVS1_Strength(RNA) or BP7(RNA) codes instead.	cspec
PS4	Not met	The PALB2 VCEP v1.2.0 requires case-control data with p≤0.05 and OR≥3 (or lower 95% CI≥1.5) for PS4. No case-control study specific to NM_024675.3:c.1684+1G>A was identified. While the variant has been observed in affected individuals submitted to ClinVar, these observations lack matched control denominator data and do not constitute a formal case-control study. Proband counting (PS4_Moderate) is not permitted under this VCEP.	clinvar cspec
PS5	N/A	Under the PALB2 VCEP framework, PP5 is explicitly designated 'Not Applicable for this VCEP' as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PS5 in the generic ACMG/AMP framework serves a similar function and is not independently assessed under the VCEP.	cspec
PM1	N/A	The PALB2 VCEP v1.2.0 specifies that PM1 is not applicable because missense pathogenic variation in PALB2 is not yet confirmed as a mechanism of disease.	cspec
PM2	Met	NM_024675.3:c.1684+1G>A is absent from gnomAD v2.1 and v4.1. Under the PALB2 VCEP v1.2.0, PM2 is applied at Supporting strength (not Moderate) when the variant frequency is ≤0.000333% (1/300,000) in gnomAD v4. The variant meets this threshold as it is completely absent from both gnomAD datasets.	gnomad_v2 gnomad_v4 cspec
PM5	Met	Under the PALB2 VCEP v1.2.0, PM5_Supporting is applied to splice variants with premature termination codons upstream of p.Tyr1183 when PVS1_VS(RNA) is applied based on high-quality observed splicing impact and the variant is NMD-prone. NM_024675.3:c.1684+1G>A is a canonical +1 splice site variant in intron 4 that has been shown to cause aberrant splicing by RNA analysis (PMID:30890586). The resulting transcript is predicted to introduce a premature termination codon far upstream of the p.Tyr1183 boundary and is expected to be NMD-prone, satisfying the VCEP PM5_Supporting conditions.	cspec PMID:30890586
PM6	N/A	The PALB2 VCEP v1.2.0 specifies that PM6 is not applicable for autosomal dominant or autosomal recessive PALB2 conditions, as informative de novo occurrences have not been observed and de novo AR conditions are unlikely to be informed by phase.	cspec
PP1	Not met	No co-segregation data in affected family members was identified for NM_024675.3:c.1684+1G>A. The PALB2 VCEP v1.2.0 requires quantitative co-segregation analysis (LOD scores or Bayes Factors) for autosomal dominant conditions, or affected relative counts for autosomal recessive conditions. Neither type of evidence was found in ClinVar submissions, publications, or the exploratory evidence search.	cspec clinvar
PP2	N/A	The PALB2 VCEP v1.2.0 specifies that PP2 is not applicable because missense variation is not yet confirmed or refuted as a mechanism of disease for PALB2.	cspec
PP3	Not met	The PALB2 VCEP v1.2.0 PP3 rule for splicing variants is: 'Predicted impact via splicing (SpliceAI ≥0.2) for intronic variants OUTSIDE of donor and acceptor 1,2 sites.' NM_024675.3:c.1684+1G>A is a +1 donor site variant, which is AT a donor 1,2 site, not outside it. Therefore PP3 does not apply per VCEP rules. Additionally, the VCEP notes that 'PP3 for splice predictions may not be applied in addition to PVS1' to avoid double-counting the same splice-effect evidence. While SpliceAI predicts a high-impact donor loss (max delta = 0.94), this evidence is already captured under PVS1.	cspec spliceai
PP4	N/A	The PALB2 VCEP v1.2.0 specifies that PP4 is not applicable for autosomal dominant PALB2 conditions, as breast cancer is a disease with multiple genetic etiologies and there are no features that can readily distinguish hereditary from sporadic causes.	cspec
PP5	N/A	The PALB2 VCEP v1.2.0 designates PP5 as 'Not Applicable for this VCEP' as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. This criterion is not for use under the PALB2 VCEP framework.	cspec
BA1	Not met	Under the PALB2 VCEP v1.2.0, BA1 requires Grpmax Filtering AF >0.1% in gnomAD v4. NM_024675.3:c.1684+1G>A is absent from gnomAD v4.1 (0 alleles). The BA1 threshold is not met.	gnomad_v4 cspec
BS1	Not met	Under the PALB2 VCEP v1.2.0, BS1 requires Grpmax Filtering AF >0.01% in gnomAD v4. NM_024675.3:c.1684+1G>A is absent from gnomAD v4.1. The BS1 threshold is not met.	gnomad_v4 cspec
BS2	Not met	The PALB2 VCEP v1.2.0 applies BS2 in the context of Fanconi anemia (recessive condition) using a points-per-proband system. No observation of this variant in a healthy individual (without Fanconi anemia) in a biallelic or appropriate heterozygous context was identified. Without specific proband data satisfying the VCEP BS2 tables, this criterion cannot be met.	cspec
BS3	N/A	The PALB2 VCEP v1.2.0 specifies that BS3 (protein-level functional studies showing no damaging effect) is not applicable. For RNA-level evidence of normal splicing, the VCEP directs use of BP7(RNA) instead.	cspec
BS4	Not met	The PALB2 VCEP v1.2.0 applies BS4 based on quantitative co-segregation analysis showing lack of segregation (LOD ≤-1.28 for Strong, ≤-0.64 for Moderate, ≤-0.32 for Supporting). No evidence of non-segregation was identified for NM_024675.3:c.1684+1G>A. No family studies demonstrating absence of the variant in affected relatives were found.	cspec
BP1	Not met	The PALB2 VCEP v1.2.0 BP1 criterion applies specifically to missense variants in PALB2, based on the low rate of functional missense variants. NM_024675.3:c.1684+1G>A is a canonical splice site variant, not a missense variant, and therefore BP1 does not apply.	cspec
BP2	N/A	The PALB2 VCEP v1.2.0 specifies that BP2 is not applicable; the ATM PM3/BP2 table should be used instead (ATM-specific).	cspec
BP4	Not met	The PALB2 VCEP v1.2.0 BP4 rule for splicing variants requires 'No predicted impact via splicing (SpliceAI ≤0.1).' NM_024675.3:c.1684+1G>A has a SpliceAI max delta score of 0.94 (donor loss = 0.94), well above the 0.1 threshold. BP4 is not met.	spliceai cspec
BP5	N/A	The PALB2 VCEP v1.2.0 specifies that BP5 is not applicable. The VCEP notes that cases with multiple pathogenic variants have been observed with no noticeable difference in phenotype, and PALB2 has moderate penetrance with higher tolerance in the general population.	cspec
BP6	N/A	The PALB2 VCEP v1.2.0 designates BP6 as 'Not Applicable for this VCEP' as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	Not met	The PALB2 VCEP v1.2.0 BP7 (in silico) is limited to synonymous and deep intronic variants beyond +7 (donor) and -21 (acceptor). NM_024675.3:c.1684+1G>A is at the +1 donor position, which is within the excluded canonical splice region. BP7(RNA) would require observed lack of aberrant splicing; however, RNA analysis in PMID:30890586 demonstrated that c.1684+1G>A does cause aberrant splicing. Therefore neither BP7 nor BP7(RNA) is met.	cspec PMID:30890586
BP3	N/A	The PALB2 VCEP v1.2.0 specifies BP3 is not applicable as small in-frame deletions/insertions are neither confirmed nor refuted as a mechanism of pathogenicity for PALB2, and PALB2 is not considered to have repetitive regions without known function.	cspec
PM3	N/A	Skipped per workflow instruction. While PM3 is applicable under the PALB2 VCEP for Fanconi anemia (biallelic context), no evidence of this variant in trans with another PALB2 pathogenic variant in a Fanconi anemia patient was identified in available materials.	cspec
PM4	N/A	The PALB2 VCEP v1.2.0 specifies PM4 is not applicable. It is only used for stop-loss variants under this framework, and c.1684+1G>A is a canonical splice site substitution, not a stop-loss variant.	cspec

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