16-23607860-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 10 ACMG points: 10P and 0B. PM3PVS1
This summary comes from the ClinGen Evidence Repository: The c.3350+4A>G variant in PALB2 is an intronic variant proximal to the exon 12 canonical splice donor site. This variant has a minor allele frequency in gnomAD v2.1.1 of 0.000008796 in the non-Finnish European population (PM2_Supporting, BS1, and BA1 are not met). This intronic variant is proximal to the exon 12 canonical splice donor site. RNA analysis demonstrated that the variant impacts splicing, generating two abnormal products: r.3202_ 3350del149, in which exon 12 is skipped, and r.3350insGCAG, which utilizes a cryptic splice donor site, both of which result in translational frameshifts. The resulting mRNA products are not expected to be susceptible to nonsense-mediated decay, but impacts the WD40 domain, which is a functionally important region (PMID:17200671, additional information in Reinhard Kalb dissertation (urn:nbn:de:bvb:20-opus-25823)). This variant has been detected in an individual with Fanconi Anemia that is compound heterozygous for this variant and a pathogenic variant confirmed in trans by parental testing (PALB2 c.2393_2394insCT (p.Thr799fs), PMID:17200671). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant hereditary breast and pancreatic cancer and autosomal recessive FANCN based on the ACMG/AMP criteria applied as specified by the HBOP VCEP. (PVS1(RNA), PM3) LINK:https://erepo.genome.network/evrepo/ui/classification/CA269618/MONDO:0016419/020
Frequency
Consequence
NM_024675.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251418Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135882
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461526Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727058
GnomAD4 genome
ClinVar
Submissions by phenotype
Familial cancer of breast Pathogenic:6
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This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 17200671]. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad Internal Data]. -
This sequence change falls in intron 12 of the PALB2 gene. It does not directly change the encoded amino acid sequence of the PALB2 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is present in population databases (rs180177136, gnomAD 0.0009%). This variant has been observed in individual(s) with breast cancer and medulloblastoma and/or Fanconi anemia (PMID: 17200671, 26976419, 28828701, 29753700, 32339256). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS12+4A>G. ClinVar contains an entry for this variant (Variation ID: 126737). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects PALB2 function (PMID: 17200671, 23934222). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the activation of a cryptic splice site and introduces a new termination codon and introduces a new termination codon (internal data). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
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The c.3350+4A>G variant in PALB2 is an intronic variant proximal to the exon 12 canonical splice donor site. This variant has a minor allele frequency in gnomAD v2.1.1 of 0.000008796 in the non-Finnish European population (PM2_Supporting, BS1, and BA1 are not met). This intronic variant is proximal to the exon 12 canonical splice donor site. RNA analysis demonstrated that the variant impacts splicing, generating two abnormal products: r.3202_ 3350del149, in which exon 12 is skipped, and r.3350insGCAG, which utilizes a cryptic splice donor site, both of which result in translational frameshifts. The resulting mRNA products are not expected to be susceptible to nonsense-mediated decay, but impacts the WD40 domain, which is a functionally important region (PMID: 17200671, additional information in Reinhard Kalb dissertation (urn:nbn:de:bvb:20-opus-25823)). This variant has been detected in an individual with Fanconi Anemia that is compound heterozygous for this variant and a pathogenic variant confirmed in trans by parental testing (PALB2 c.2393_2394insCT (p.Thr799fs), PMID: 17200671). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant hereditary breast and pancreatic cancer and autosomal recessive FANCN based on the ACMG/AMP criteria applied as specified by the HBOP VCEP. (PVS1(RNA), PM3) -
Hereditary cancer-predisposing syndrome Pathogenic:3
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This variant causes an A to G nucleotide substitution at the +4 position of intron 12 of the PALB2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. A minigene splicing assay has shown that this variant results in two out-of-frame splicing products (PMID: 34846068), and a Fanconi anemia patient-derived cell line containing this variant and a frameshift PALB2 co-variant has been shown to have no detectable PALB2 full-length protein and to exhibit defects in cellular DNA response (PMID: 17200671, 20153123). This variant has been reported in at least six individuals affected with breast cancer (PMID: 26976419, 28828701, 32339256, 33120919, 33910496), two individuals affected with breast and/or ovarian cancer (PMID: 30128536), two individuals affected with pancreatic cancer (PMID: 29922827) and an individual affected with medulloblastoma (PMID: 29753700). This variant also has been reported with a pathogenic PALB2 covariant in an individual affected with Fanconi anemia (PMID: 17200671) and a homozygous carrier suspected of Fanconi anemia (PMID: 32947577). This variant has been identified in 1/251418 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PALB2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
The c.3350+4A>G intronic pathogenic mutation results from an A to G substitution 4 nucleotides after coding exon 12 in the PALB2 gene. This alteration has been detected in trans with another PALB2 mutation in an individual with Fanconi Anemia. Analysis of the mutant transcripts showed that the variant activates a cryptic donor site causing a translational frameshift with a predicted alternate stop codon (Reid S et al. Nat. Genet. 2007 Feb;39:162-4). Functional studies performed using patient samples indicate that this variant is associated with disrupted spindle assembly checkpoint activity, spontaneous micronucleation and impaired double-strand break repair capacity (Reid S et al. Nat. Genet. 2007 Feb;39:162-4; Rube CE et al. Int J Radiat Oncol Biol Phys. 2010 Oct;78(2):359-69; Nalepa G et al. J Clin Invest. 2013 Sep;123(9):3839-47). This variant has been observed in individuals with breast and pancreatic cancer (Jones S et al. Science. 2009 Apr;324:217; Zidan J et al. Breast Cancer Res. Treat. 2017 Dec;166:881-885; Zhou J et al. Cancer 2020 Jul;126(14):3202-3208). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as a disease-causing mutation. -
PALB2-related disorder Pathogenic:2
The PALB2 c.3350+4A>G variant is predicted to interfere with splicing. This variant has been documented in the compound heterozygous state in an individual with Fanconi anemia and medulloblastoma (Patient LNEY in Reid et al. 2007. PubMed ID: 17200671). This variant has also been detected in patients from several large cancer studies including pancreatic cancer (Table e3 in Hu et al. 2018. PubMed ID: 29922827) and breast and/or ovarian cancer (Table S2 in Zhou et al. 2020. PubMed ID: 32339256; eTable 2 in George et al. 2021. PubMed ID: 33646313; eTable 12 in Lu et al. 2019. PubMed ID: 30128536). A functional assay showed that this variant disrupted splicing by introducing a cryptic donor site four nucleotides downstream of exon 12 (Valenzuela-Palomo et al. 2021. PubMed ID: 34846068). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-23619181-T-C) and is interpreted as likely pathogenic by an expert curation panel in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/126737/). This variant is interpreted as pathogenic. -
Variant summary: PALB2 c.3350+4A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant creates a 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-06 in 251418 control chromosomes (gnomAD). The variant, c.3350+4A>G, has been reported in the literature in compound heterozygous state (with a frame-shift variant in trans) in a child who was affected with Fanconi Anemia Type N, and developed medulloblastoma in early childhood (Reid_2007, Rube_2010). Publications examining fibroblasts derived from this patient reported no detectable PALB2 protein, impaired double-strand break repair capacity, and defective spindle assembly checkpoint leading to aneuploidy (Reid_2007, Rube_2010, Nalepa_2013). The variant was also reported in heterozygous state in multiple patients, affected with breast- and pancreatic cancer (e.g. Tung_2016, Zidan_2017, Hu_2018, Lu_2018, Zanti_2020). These data indicate that the variant is very likely to be associated with disease. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and all laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:2
The PALB2 c.3350+4A>G variant has been reported in the published literature in individuals with breast cancer (PMID: 33120919 (2020), 32339256 (2021), 30128536 (2018), 28828701 (2017), 26976419 (2016)), pancreatic cancer (PMID: 29922827 (2018)), medulloblastoma (PMID: 29753700 (2018)) and Fanconi anemia, including one homozygote (PMID: 32947577 (2021)) and one compound heterozygote carrying a second pathogenic PALB2 variant (PMID: 17200671 (2007)). Additionally, functional studies demonstrated that this variant disrupted PALB2 mRNA splicing (PMID: 34846068 (2022), 17200671 (2007)). The frequency of this variant in the general population, 0.000004 (1/251418 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on PALB2 mRNA splicing yielded predictions that this variant may result in the gain of a cryptic splice site without affecting the natural splice sites. Based on the available information, this variant is classified as likely pathogenic. -
Non-canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate a damaging effect: absence of PALB2 protein in fibroblasts, impaired double strand break repair, disrupted spindle assembly checkpoint activity (Reid et al., 2007; Rube et al., 2010; Nalepa et al., 2013); Observed in individuals with personal and/or family history of PALB2-related cancers (Tung et al., 2016; Zidan et al., 2017; Hu et al., 2018; Zhou et al., 2020; Zanti et al., 2020; George et al., 2021); Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21165770, 33120919, 20153123, 24870022, 25525159, 26976419, 28828701, 19264984, 29753700, 23934222, 17200671, 33646313, 32339256, 29922827, 34846068) -
Breast-ovarian cancer, familial, susceptibility to, 5 Pathogenic:1
This sequence change falls in intron 12 of the PALB2 gene. It does not directly change the encoded amino acid sequence of the PALB2 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C‐terminus of the protein. This variant not observed at a significant frequency in large population cohorts (gnomAD) nor in our local database . This variant has been reported as in heterozygous state in individuals affected with breast/ovarian cancer (PMID: 26976419, 28828701, 30128536), pancreatic cancer (PMID: 19264984), and compound heterozygous with Fanconi anemia/medulloblastoma (PMID: 17200671, 20153123). This variant is also known as IVS12+4A>G. ClinVar contains an entry for this variant (Variation ID: 126737) bymany clinical diagnostic laboratories which submitted clinical‐significance assessments for this variant to ClinVar after 2014, and all laboratories classified the variant as pathogenic/likely pathogenic. For these reasons, this variant has been classified as Pathogenic. -
Malignant tumor of breast Pathogenic:1
PVS1(RNA), PM3 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at