ClinVar Genomic variation as it relates to human health

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

This alteration is classified as 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.

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

The PALB2 p.Ile309Val variant was identified in 41 of 4986 proband chromosomes (frequency: 0.008) from individuals or families with breast Cancer of African-American, Chinese, Malaysian and Singaporean descent and was present in 50 of 4390 control chromosomes (frequency: 0.011) from healthy individuals (Ding 2011, Li 2015, Phuah 2013, Wong-Brown 2014, Zheng 2012, Sluiter 2009). The variant was also identified in dbSNP (ID: rs3809683) as “Other”, ClinVar (benign by GeneDx, Ambry Genetics, Invitae), PALB2 Database (likely benign by Cancer Genetics Laboratory and Illumina Clinical Services Laboratory), LOVD 3.0 (8x with no classification) Zhejiang Colon Cancer Database (1x as unknown). The variant was not identified in Cosmic, MutDB, databases. The variant was further identified in the 1000 Genomes Project in 58 of 5000 chromosomes (freq. 0.01) and the NHLBI GO Exome Sequencing Project in 126 of 4394 African American alleles (freq. 0.03). The variant was identified in control databases in 932 of 277056 chromosomes at a frequency of 0.003 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). Notably the variant was identified in the African population in 690 of 24026 chromosomes (freq. 0.02) including 10 homozygous individuals. The p.Ile309 residue is not conserved in mammals and the variant amino acid (Val) is present in Macaca mulatta, Rattus norvegicus, and Mus musculus increasing the likelihood that this variant does not have clinical significance. In addition, computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant is classified as benign.

Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitters to LOVD: Marc Tischkowitz, Melissa DeRycke, Yukihide Momozawa.