ClinVar Miner

Submissions for variant NM_000249.4(MLH1):c.117-10G>A

gnomAD frequency: 0.00007  dbSNP: rs576724240
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000227602 SCV000284008 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-12-09 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000583139 SCV000689793 likely benign Hereditary cancer-predisposing syndrome 2017-09-14 criteria provided, single submitter clinical testing
GeneDx RCV001722211 SCV000728963 likely benign not provided 2020-02-28 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24710284)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000601988 SCV000917653 uncertain significance not specified 2017-12-26 criteria provided, single submitter clinical testing Variant summary:The MLH1 c.117-10G>A variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a damaging outcome for this variant. 3/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 15/246218 control chromosomes (gnomAD), only observed in the East Asian subpopulation at a frequency of 0.00087 (15/17248). This frequency is about 1.2 times the estimated maximal expected allele frequency of a pathogenic MLH1 variant (0.0007105), suggesting this is possibly a benign polymorphism found primarily in the populations of East Asian origin. This variant has been reported in one Lynch Syndrome family without strong evidence for or against pathogenicity and classified as variant of unknown significance (Liu_2014). In addition, one clinical diagnostic laboratory has classified this variant as likely benign. Taken together, this variant is classified as variant of unknown significance-possibly benign.
Sema4, Sema4 RCV000583139 SCV002528629 likely benign Hereditary cancer-predisposing syndrome 2021-09-10 criteria provided, single submitter curation
All of Us Research Program, National Institutes of Health RCV003998737 SCV004825449 likely benign Lynch syndrome 2023-12-13 criteria provided, single submitter clinical testing

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