ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4930G>A (p.Asp1644Asn)

gnomAD frequency: 0.00002  dbSNP: rs137853999
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000340816 SCV000395665 likely benign Tuberous sclerosis syndrome 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000475549 SCV000544500 likely benign Tuberous sclerosis 2 2025-01-23 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000475549 SCV002040233 likely benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV002338902 SCV002642698 likely benign Hereditary cancer-predisposing syndrome 2023-01-20 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University RCV000475549 SCV001423573 likely pathogenic Tuberous sclerosis 2 2022-08-05 flagged submission clinical testing According to ACMG GL 2015, this variant located in GAP domain (PM1), Asp1644Tyr determined to be pathogenic (PM5), multiple lines of computational evidence support a deleterious effect (PP3). Also detected in the patient with clinically definitive tuberous sclerosis complex (PP4) and cosegregation with disease in multiple affected family members (PP1).

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