ClinVar Miner

Submissions for variant NM_000368.5(TSC1):c.1250C>T (p.Thr417Ile) (rs77464996)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000422201 SCV000520926 likely benign not specified 2016-12-02 criteria provided, single submitter clinical testing 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000422201 SCV000540597 uncertain significance not specified 2017-01-25 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant has been reported in 4 papers in HGMD but comments suggest not pathogenic as it has been seen in unaffected individuals and there was no LOH in tumors of carriers. It has a Max MAF of 0.05% in ExAC (4 alleles) and 0.03% in gnomAD (6 alleles). The variant is present in ClinVar but with no classification. The variant is predicted to be benign by prediction tools. This AA is not conserved and 3 mammals have an Ile at this position.
Invitae RCV000988278 SCV000562472 benign Tuberous sclerosis 1 2019-12-31 criteria provided, single submitter clinical testing
Mendelics RCV000988278 SCV001137937 uncertain significance Tuberous sclerosis 1 2019-05-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV001010542 SCV001170758 likely benign Hereditary cancer-predisposing syndrome 2018-07-27 criteria provided, single submitter clinical testing Co-occurence with mutation in same gene (phase unknown);Does not segregate with disease in family study (genes with incomplete penetrance);Subpopulation frequency in support of benign classification
Illumina Clinical Services Laboratory,Illumina RCV001165673 SCV001327891 benign Focal cortical dysplasia type II 2017-04-27 criteria provided, single submitter clinical testing 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 was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV000988278 SCV001327892 benign Tuberous sclerosis 1 2017-04-27 criteria provided, single submitter clinical testing 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Tuberous sclerosis database (TSC1) RCV000041999 SCV000065780 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC1) RCV000055012 SCV000083230 not provided Urinary bladder cancer no assertion provided curation

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