Interpretation
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Variants Of Unknown Significance (VUS) Policy And Interpretation
- What is the protocol for interpreting a variation as a VUS? HelpDescription of how the laboratory handles Variants of Unknown Significance. This may be a general statement for the laboratory and not specific to this test.
- Variations are first classified based on frequency (according to databases such as 1000 Genomes and GnomAD). Rare variations are classified as VUS if: 1) the variation has not been reported previously and available information (effect prediction models, conservation scores and patient data) does not allow other classification; 2) there are conflicting or inconclusive reports from published studies regarding the possible effect of the variation. Where possible, ACMG recommendations for variant classification are applied.
- What software is used to interpret novel variations? HelpList of the software applications that the lab uses to interpret novel variants. Examples for medical molecular genetics interpretation include: Melina II, MEME Suite, VISTACartagenia Bench, Alamut, SIFT, PolyPhen, Align-GVGD, GeneSplicer, laboratory proprietary internal software.
- Alamut® Visual (includes splice site prediction tools, SIFT, PolyPhen2, MutationTaster, frequency data).
- What is the laboratory's policy on reporting novel variations? HelpDescription of how the lab reports novel variations, it may include who gets contacted and how (ex. person ordering the test will be contacted via telephone as soon as VUS is identified).
- Novel variations are interpreted in the context of the patient’s data as well as information known about the gene that it was found in. If possible association with patient’s phenotype is suspected, novel variations are reported with a short description of the possible effect and population frequencies.
- Are family members with defined clinical status recruited to assess
significance of VUS without charge?HelpDoes the laboratory offer testing for a variant of unknown significance to family members, free of charge? (Is test offered to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS?)
- Not provided
- Will the lab re-contact the ordering physician if variant interpretation
changes? HelpDescription of laboratory procedures to monitor and address reinterpretation of genetic tests results over time, after issuing the report. Does laboratory systematically re-evaluate prior interpretations and generate new reports, or does the person ordering the test need to periodically recontact the labortory to inquire about changes in test interpretation?
- Not provided
Research
- Is research allowed on the sample after clinical testing is
complete?HelpAfter clinical testing is complete, does the laboratory perform any research testing using the submitted specimen? (Quality control is not considered as research for this question.)
- Not provided
IMPORTANT NOTE: NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in the GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.
