ClinVar Genomic variation as it relates to human health

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

PALB2:c.2379C>T is present in 0.0081% in the large population studies (GnomAd). The deep exonic variant is predicted to create a de novo donor splice site in exon 5 by in silico splicing tools. Functional RNA study has shown that the variant causes an insignificant splicing aberration leading to out-of-frame transcript (PMID: 35806449, 31642931). Therefore the variant was classified as likely benign (ACMG/AMP: BS3-Stand alone, BS1, PP3).

Variant summary: PALB2 c.2379C>T alters a non-conserved nucleotide resulting in a synonymous change. 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. In contrast, one recently published functional study reported this variant among those with no impact on RNA splicing (Karam_2019). The authors considered the in-silico splicing predictions as a false positive evidence category and reported re-classifying this variant from a VUS to likely benign based on their study. The variant allele was found at a frequency of 7.4e-05 in 256744 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in PALB2 causing Hereditary Breast And Ovarian Cancer Syndrome (7.4e-05 vs 0.00016), allowing no conclusion about variant significance. c.2379C>T has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (example, Catucci_2014, Damiola_2015, Thompson_2015, Borecka_2016, Decker_2017 etc.). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. In addition, this variant was found in four women in FLOSSIES database of cancer free women older than age 70, suggesting that the variant could be benignTo our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 12 clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar classified as VUS (n=5), Likely Benign (n=6) and Benign (n=1). Based on the evidence outlined above, the variant was classified as benign.

This variant is associated with the following publications: (PMID: 26564480, 26283626, 24556926, 28779002, 31642931)

In the published literature, this variant has been reported in individuals with breast cancer (PMIDs: 35264596 (2022), 35806449 (2022), 28779002 (2017), 26564480 (2015), 26283626 (2015), 24556926 (2014)) and pancreatic cancer (PMID: 27106063 (2016)). Experimental studies on PALB2 mRNA splicing report the variant has no significant effect on splicing, however additional studies are needed to determine the global effect of this variant on PALB2 function (PMIDs: 35806449 (2022), 31642931 (2019)). The frequency of this variant in the general population, 0.00011 (14/129160 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, we are unable to determine the clinical significance of this variant.

PALB2: PP3, BS1:Supporting, BS3:Supporting

The PALB2 p.Gly793= variant was identified in 2 of 5146 proband chromosomes (frequency: 0.0004) from individuals or families with breast cancer and was not identified in 3996 control chromosomes from healthy individuals (Catucci 2014, Thompson 2015). The variant was also identified in dbSNP (ID: rs377626805) as "With other allele", ClinVar (classified as likely benign by Invitae, Ambry Genetics and one clinical laboratory; as uncertain significance by five submitters), and in LOVD 3.0 (1x) database. The variant was identified in control databases in 22 of 277202 chromosomes at a frequency of 0.00008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 24034 chromosomes (freq: 0.00004), Other in 1 of 6466 chromosomes (freq: 0.0002), Latino in 3 of 34412 chromosomes (freq: 0.00009), European in 15 of 126706 chromosomes (freq: 0.0001), Ashkenazi Jewish in 1 of 10150 chromosomes (freq: 0.0001), and South Asian in 1 of 30778 chromosomes (freq: 0.00003), while the variant was not observed in the East Asian, and Finnish, populations. The p.Gly793= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs outside of the splicing consensus sequence and 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz.