ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.6006+8T>C (rs56019194)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000465701 SCV000558381 likely benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Color RCV000580088 SCV000682297 likely benign Hereditary cancer-predisposing syndrome 2017-01-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV001193663 SCV001362657 likely benign not specified 2019-10-04 criteria provided, single submitter clinical testing Variant summary: ATM c.6006+8T>C alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools via ALAMUT predict no significant impact on normal splicing. Another in-silico tool, TraP (Transcript-inferred Pathogenicity score) predicts the variant to be benign (Gelfman_2017). However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00011 in 250578 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in ATM causing Breast Cancer or Ataxia Telangectasia, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.6006+8T>C in individuals affected with AT/Breast Cancer and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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