Description
The MSH6 p.Thr118= variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors databases. The variant was identified in dbSNP (ID: rs558590898) as “With Likely benign allele”, ClinVar (as likely benign by Invitae, Partners HealthCare Personalized Medicine, Ambry Genetics, and Color), and Clinvitae (3x). The variant was identified in control databases in 4 of 246272 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 15304 chromosomes (freq: 0.00007), European (Non-Finnish) in 2 of 111720 chromosomes (freq: 0.00002), and East Asian in 1 of 17248 chromosomes (freq: 0.000058); it was not observed in the Other, Latino, Ashkenazi Jewish, Finnish, and South Asian populations. The p.Thr118= 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.
# | Sample | Method | Observation |
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Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences |
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1 | unknown | yes | not provided | not provided | not provided | | not provided | not provided | not provided | not provided |