Total submissions: 12
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Labcorp Genetics |
RCV000476070 | SCV000548751 | likely benign | Hereditary spastic paraplegia 49 | 2024-01-29 | criteria provided, single submitter | clinical testing | |
Gene |
RCV000498170 | SCV000589925 | likely benign | not specified | 2017-12-28 | 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. |
Genome Diagnostics Laboratory, |
RCV001848808 | SCV002105919 | likely benign | Hereditary spastic paraplegia | 2019-05-01 | criteria provided, single submitter | clinical testing | |
Ce |
RCV001573137 | SCV004135224 | likely benign | not provided | 2024-03-01 | criteria provided, single submitter | clinical testing | TECPR2: BP1, BP4 |
Ambry Genetics | RCV004022706 | SCV004963784 | likely benign | Inborn genetic diseases | 2022-04-08 | 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. |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000498170 | SCV005185333 | likely benign | not specified | 2024-05-08 | criteria provided, single submitter | clinical testing | Variant summary: TECPR2 c.1644T>G (p.Asn548Lys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00097 in 194180 control chromosomes, predominantly at a frequency of 0.0018 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 2 fold of the estimated maximal expected allele frequency for a pathogenic variant in TECPR2 causing Hereditary Spastic Paraplegia, Type 49 phenotype (0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. To our knowledge, no occurrence of c.1644T>G in individuals affected with Hereditary Spastic Paraplegia, Type 49 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 408917). Based on the evidence outlined above, the variant was classified as likely benign. |
Breakthrough Genomics, |
RCV001573137 | SCV005211473 | likely benign | not provided | criteria provided, single submitter | not provided | ||
Laboratory of Diagnostic Genome Analysis, |
RCV001573137 | SCV001798541 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Clinical Genetics DNA and cytogenetics Diagnostics Lab, |
RCV001573137 | SCV001973299 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Natera, |
RCV000476070 | SCV002091110 | benign | Hereditary spastic paraplegia 49 | 2019-10-21 | no assertion criteria provided | clinical testing | |
Genome |
RCV000476070 | SCV003931200 | not provided | Hereditary spastic paraplegia 49 | no assertion provided | phenotyping only | Variant classified as Uncertain significance and reported on 06-22-2017 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. | |
Prevention |
RCV003972758 | SCV004789113 | likely benign | TECPR2-related disorder | 2022-12-15 | no assertion criteria provided | clinical testing | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). |