ClinVar

Description

The CDH1 p.Thr115Thr variant was identified in 6 of 380 proband chromosomes (frequency: 0.016) from individuals or families with gastric cancer, other cancer types and normal individuals (Garziera 2013) and was present in 1 of 40 control chromosomes (frequency: 0.025) from healthy individuals (Berx 1997). The variant was also identified in dbSNP (ID: rs1801023) as “With other allele”, ClinVar (6x, as benign by Invitae, GeneDx, Ambry Genetics, Prevention Genetics, Color Genomics, as likely benign by Illumina), Clinvitae (3x as benign ), Zhejiang Colon Cancer Database. The variant was not identified in Cosmic, MutDB, databases. The variant was identified in control databases in 991 of 276784 (5 homozygous) chromosomes at a frequency of 0.0036 in the following populations: African in 12 of 24020 chromosomes (freq. 0.0005), other in 26 of 6460 chromosomes (freq. 0.004), Latino in 72 of 34410 chromosomes (freq. 0.002), European in 518 of 126334 chromosomes (freq. 0.0041), Ashkenazi Jewish in 109 of 10130 chromosomes (freq. 0.01), East Asian in 3 of 18868 chromosomes (freq. 0.00016), Finnish in 15 of 25784 chromosomes (freq. 0.0006), and South Asian in 236 of 30778 chromosomes (freq. 0.0076),.increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The p.Thr115Thr 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. In addition, 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 the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.