Submissions for variant NM_000391.4(TPP1):c.1044C>T (p.Ala348=)

gnomAD frequency: 0.00982  dbSNP: rs35706972

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000118649	SCV000169045	benign	not specified	2012-05-17	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.
Invitae	RCV000675457	SCV000284803	benign	not provided	2024-01-31	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000118649	SCV000303958	benign	not specified		criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002312512	SCV000846334	benign	Inborn genetic diseases	2016-05-03	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: 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.
Illumina Laboratory Services, Illumina	RCV001102828	SCV001259520	likely benign	Neuronal ceroid lipofuscinosis 2	2018-01-13	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.
Athena Diagnostics Inc	RCV000118649	SCV001474928	benign	not specified	2020-04-06	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000675457	SCV002544537	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	TPP1: BP4, BP7, BS1, BS2
Fulgent Genetics, Fulgent Genetics	RCV002498539	SCV002811943	likely benign	Neuronal ceroid lipofuscinosis 2; Autosomal recessive spinocerebellar ataxia 7	2021-09-21	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000118649	SCV000153063	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Mayo Clinic Laboratories, Mayo Clinic	RCV000675457	SCV000801142	benign	not provided	2017-05-15	no assertion criteria provided	clinical testing
Natera, Inc.	RCV001102828	SCV001455833	benign	Neuronal ceroid lipofuscinosis 2	2020-09-16	no assertion criteria provided	clinical testing